For a thematic listing of currently supported free software, look at the Free Software Menu.
Which version of SilentKnight and other apps do you need?
Which apps for which macOS, from El Capitan to Sequoia? details which versions you should use, according to macOS.

App for Ventura and later

Liviable – run GUI Linux distros in virtual machines (Apple silicon only)

Product page.
Liviable 1.0.5 (b5) (Apple silicon only, for Ventura and Sonoma)

App for Monterey and later

Skint – a watchful eye on security settings

Product page.
Skint 1.08 (Universal App for Monterey, Ventura, Sonoma and Sequoia only)

Viable – run macOS in virtual machines (Apple silicon only)

Product page.
Viable 1.0.12 (b12) (Apple silicon only, for Monterey, Ventura and Sonoma)
Sandboxed and locked-down version:
ViableS 1.0.12 (b12) (Apple silicon only, for Monterey, Ventura and Sonoma)

Vimy – double-clickable macOS virtual machines (Apple silicon only)

Product page.
Vimy 0.7 (fourth beta) (Apple silicon only, for Monterey, Ventura and Sonoma)

Apps for Big Sur and later

Versatility – archive and unarchive saved versions to protect and preserve them

Product page.
Versatility 1.0 (Universal App for Big Sur, Monterey, Ventura and Sonoma)

The Time Machine Mechanic (T2M2) – a quick but thorough check of Time Machine backing up (version 2)

Product page.
T2M2 2.02 (Universal App for Big Sur, Monterey, Ventura and Sonoma)

Spotcord – build vocabularies of Spotlight keywords

Product Page
Spotcord 0.8, second beta (Universal App for Big Sur, Monterey, Ventura and Sonoma)

Cormorant – compression and decompression using Apple Archive

Product page.
Cormorant 1.5 (Universal App for Big Sur, Monterey, Ventura and Sonoma)

Sparsity – create and find APFS sparse files

Product page.
Sparsity 1.3 (Universal App for Big Sur, Monterey, Ventura and Sonoma).

App for Catalina and later

XProCheck – check on XProtect Remediator scans completed and reported in the log

Product Page.
XProCheck 1.6 (Universal App for Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Apps for High Sierra and later

Signet – scans and checks bundle signatures

Product page.
Signet 1.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur and Monterey)

Apps for Mojave and later

Nalaprop – multilingual natural language parsing

Product page.
Nalaprop 1.3 (Universal App for Mojave, Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Metamer – a simple metadata editor
Product page.
Metamer 1.5 (Universal App for Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

Apps (for Macs running El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Some are now available using AutoPkg: see this article for details.

SilentKnight – automatic checking of security systems

Product page.
SilentKnight 1.21 (Universal App for El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur, Monterey and Ventura)
SilentKnight 2.11 (Universal App for Catalina to Sequoia)

silnite – command tool equivalent of SilentKnight to check security systems

Product page.
silnite 10 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

LockRattler – a quick check of your security systems
Product page.
LockRattler 4.37 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey and Ventura)

SystHist – lists full system and security update installation history
Product page.
SystHist 1.20 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Dintch – check the integrity of your files
Product page.
Dintch 1.6 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

Fintch – drag and drop file integrity management
Product page.
Fintch 1.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

cintch – command tool to check file integrity
Product page.
cintch 3 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

32-bitCheck – checks installed apps, code bundles, command tools and more for those which are 32-bit
Product page.
32-bitCheck 1.8 (El Capitan, Sierra, High Sierra, Mojave and Catalina)

Cirrus – takes control of iCloud, investigates and diagnoses its problems
Product page.
Cirrus 1.14 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)
Cirrus 1.15 (Universal App for Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Precize – looks deep into files, bundles and folders to show their full size including extended attributes, provides macOS Bookmarks and volfs paths as enduring file references, and detailed information contained in Bookmarks and Aliases
Product page.
Precize 1.12 (Universal App for El Capitan and Sierra)
Precize 1.15 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Revisionist – opens up the full power of the macOS versioning system
Product page.
Revisionist 1.9 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

xattred – full-featured extended attribute editor, can also add quarantine xattrs
Product page.
xattred 1.5 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

Scrub – cleans folders and volumes of potentially leaking sensitive data
Product page.
Scrub 1.3 (Universal Binary for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

Aquiline Check – clear your QuickLook cache to protect your privacy

Aquiline Check lets you empty your QuickLook cache to remove all trace of thumbnails and previews of old documents, such as those from encrypted disks. It can also disable caching, and check that the cache is being managed safely. Second beta release, with Aquiliner menubar companion app now in version 1.0.
Aquiline Check 1.0b2a (El Capitan, Sierra and High Sierra only)

Bailiff – menubar control over whether iCloud documents are kept in local storage
Product page.
Bailiff 1.5 (Universal App for El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

DeepTools – three quick and simple tools to preserve versions associated with your documents when copying or moving them
Product page.
DeepTools 1.4 (Universal App for El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur, Monterey and Ventura)

SearchKey – adds metadata to any file to aid Spotlight search
Product page.
SearchKey 1.5 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

SearchKeyLite – lightweight tool to add metadata to documents to aid Spotlight search
Product page.
SearchKeyLite 1.5 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

UTIutility – UTI scanning and conversion utility
Product page.
UTIutility 1.1 (Universal App for El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)
UTIutility 1.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

alisma – a command tool to create Finder aliases, and to resolve them to full paths
Product page.
alisma 4 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

cmpxat – a command tool to compare all the extended attributes (xattrs) between two files, reporting any differences
Product page.
cmpxat 4 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

Apps (for Macs running Sierra, High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

Albinoz has revised and repackaged Alex Karahalios’ original shell script and Automator workflow to convert JPEG images to HEIF/HEIC format. They are both available from this article, which explains more fully.

Stibium – new SSD performance benchmarking utility
Product page.
Stibium 1.1 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma).

Ulbow – log browser designed for ease of use without sacrificing power
Product page.
Ulbow 1.7 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey).
Ulbow 1.10 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma).

Mints – collection of custom log browsers and tools
Product page.
Mints 1.9 (Universal App for Sierra).
Mints 1.19 (Universal App for High Sierra, Mojave and Catalina).
Mints 1.20 (Universal App for Big Sur, Monterey, Ventura, Sonoma and Sequoia).

Spundle – create, resize and compact sparse bundles
Product page.
Spundle 1.5 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur, Monterey and Ventura)
Spundle 1.8 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

ArchiChect – drag-and-drop check of 64-bit, quarantine, signatures and notarization
Product page.
ArchiChect 2.5 (Universal App for Big Sur, Monterey, Ventura and Sonoma)

The Time Machine Mechanic (T2M2) – a quick but thorough check of Time Machine backing up (version 1)
Product page.
T2M2 1.19 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Consolation – a unified log browser
Product page.
Consolation 3.13 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey).

Podofyllin – lightweight PDF viewer and analyser
Product page.
Podofyllin 1.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia).

Alifix – refreshes Aliases and identifies broken Aliases
Product page.
Alifix 1.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma).

DelightEd – Rich Text (RTF) editor with special Dark Mode features and interlinear text
Product page.
DelightEd 2.3 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura, Sonoma and Sequoia)

Taccy – troubleshoot privacy problems
Product page.
Taccy 1.15 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

RouteMap and Whither – performance analysis for apps, scripts, and more
Product page.
The Signpost Kit 3 (Universal App bundle for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)
RouteMap 1.0b4 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Pratique – simple utility to mark document quarantine flags as clear
Product page.
Pratique 1.2 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Sandstrip – strips unwanted quarantine flags written by sandboxed apps
Product page.
Sandstrip 1.2 (Universal App for Sierra, High Sierra, MMojave, Catalina, Big Sur and Monterey)

Woodpile – a new type of log browser, which explores long periods from the top down
Product page.
Woodpile 1.0b6 (Sierra and High Sierra only)

RunConsolation – runs Consolation2 as root to enable log browsing when in normal user mode
Product page.
RunConsolation 1.1 (Sierra and High Sierra only)

MakeLogarchive – a utility for creating logarchives readable by Console from ‘live’ logs or raw log folders
Product page.
MakeLogarchive 0.5a1 (Sierra and High Sierra only)

RunT2M2 – runs T2M2 as root to enable assessment of Time Machine when in normal user mode
Product page.
RunT2M2 1.0 (Sierra and High Sierra only)

KeychainCheck – a quick check of your keychain setup
Product page.
KeychainCheck 1.3 (Sierra and High Sierra only)

KeychainCheck 2 – thorough diagnostics and tools for your keychain
Product page.
KeychainCheck 2.0 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Dystextia – encodes and decodes Unicode Latin text using unconventional code points
Product page.
Dystextia 1.8 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

PermissionScanner – searches folders for files which are either not writable or not readable
Product page.
PermissionScanner 1.8 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

RepairHomePermissions – repairs the permissions in your Home folder
No longer recommended: see its product page.

DispatchView – analyses the log for task dispatching issues
Product page.
DispatchView 1.0 (Sierra and High Sierra only)

Rosettavert – converts between different text encodings
Product page.
Rosettavert 1.5 (Universal App for Sierra, High Sierra, Mojave, Catalina, Big Sur and Monterey)

Apfelstrudel – check the normalisation of Unicode text, to spot potential problems with file systems other than HFS+
Product page.
Apfelstrudel 1.5 (Universal App for High Sierra, Mojave, Catalina, Big Sur, Monterey, Ventura and Sonoma)

HelpHelp – diagnose and fix problems with Help Books, and open selected ones for search

HelpHelp lists all the currently-available Help Books, and provides detailed paths and signatures for them. It can register an app of your choice, so overriding settings to use a specific Help Book. This helps you diagnose and fix problems. It will also perform a search on any selected Help Book without opening its app. Somewhere between High Sierra 10.13 and 10.13.4, Apple has made major changes to the Help system, and HelpHelp no longer works on 10.13.4. It remains compatible with Sierra 10.12.6, though.
HelpHelp 1.1 (Sierra only)

unorml – a command tool to normalise a string to any of the four Unicode forms
Product page.
unorml 5 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

Blowhole – a command tool to write into the log in macOS Sierra and later
Product page.
Blowhole 11 (Universal binary for Big Sur, Monterey, Ventura and Sonoma)

BasicPDFViewer – complete Xcode 10.1 project and source for a PDF reader and PDF Help book

A complete Xcode 10.1 project written in Swift 4.2 for a PDF reader app, using PDFKit and AppKit. See articles here for a blow-by-blow account of how to make your own. Version 1.0b3 adds Help support using a PDF Help book which can be used for almost any app. Compatible with Sierra and later, and probably El Capitan too. Copyright-free, for free use in any app, including commercial.
BasicPDFViewer 1.0b1
BasicPDFViewer 1.0b3

ScriptBase – a kickstart project for scripting using Swift 4.0 in Xcode 9.2

A complete Xcode 9.2 project written in Swift 4.0 for compatibility with El Capitan, Sierra, and High Sierra. Use as the start of a new script project, or follow its detailed step-by-step guide to create your own. Includes many useful helper functions for single-window apps. Copyright-free, for free use in any app, including commercial.
ScriptBase 1.0

Dropsy – a project prototype for droplet apps to process files using Swift 4.0 in Xcode 9.2
A complete Xcode 9.2 project for a document-based app written in Swift 4.0 and compatible with El Capitan, Sierra, and High Sierra. Includes example code which makes a copy of any files or folders dropped onto it, or opened via its menu. Complete with documentation, and for free use in any app, including commercial.
Dropsy 1.0

MacAppScaffold – a quick start Xcode project for scripting

An Xcode 8.3 project for a document-based Mac app written in Swift 3.1. Use as the basis for a new script project, or create a new project and copy across the Storyboard and ViewController.swift files from this. Includes additional helper source code. Described in this article.
Version 1.0 (release)

DispatchRider – an experimental utility to schedule and run background tasks using DAS and CTS dispatching

DispatchRider lets you set command tasks to be run automatically like Time Machine, using Apple’s ‘smart’ energy-efficient systems, rather than at fixed times using launchd.
DispatchRider 0.3b1 (Sierra and High Sierra)

Tinderbox/Storyspace Hypertext documents

Consolidated articles to help you diagnose and manage Mac problems, drawn from this blog (still growing), for Tinderbox, Storyspace and Storyspace Reader: Mac Problems 3

A Swift Scrapbook, of Swift Snippets, Swift 3.1 code for a wide range of common or useful tasks in macOS Sierra. Primarily for Tinderbox 7, although it can also be used in Storyspace: Swift Scrapbook

Ovid’s Metamorphoses, Book 1, in parallel Latin and English translation (text only): Metamorphoses Book 1
Ovid’s Metamorphoses, Book 1, in parallel Latin and English translation (with 21 paintings): Metamorphoses Book 1 illustrated
Ovid’s Metamorphoses, Book 1, in parallel Latin and English translation (with 21 paintings) for Tinderbox 7: Ovid Metamorphoses Book 1 (TB 7)
Ovid’s Metamorphoses, Book 1, in parallel Latin and English translation (with 21 paintings) for Tinderbox 7, Storyspace 3.3, and Storyspace Reader 3.3: Ovid Metamorphoses Book 1 (all)

The Salome Story: an examination of dozens of paintings, plays, texts, and even movies which tell the story of Salome, Herodias, Herod, and John the Baptist, to discover when, how, and why it changed: The Salome Story

Telling Elaine from the Lady of Shalott: full text of Tennyson’s three poems, together with thirteen superb paintings, covering these two Arthurian legends, ready to open in Storyspace, Storyspace Reader, or Tinderbox: Elaine of Astolat and The Lady of Shalott.

Tinderbox export to HTML to make a Help Book: a step-by-step guide to creating custom HTML export templates to create the files needed, then building them into a Help Book: Tinderbox 7 document and the folder ready to turn into a Help Book.

LaTeXport: writing LaTeX documents using Tinderbox. A complete set of custom export templates and prototypes for the article document class which can be modified for other types of LaTeX document: LaTeX Paper (version 2).

LaTeXport: writing LaTeX documents using Tinderbox. A complete set of custom export templates and prototypes for the superb tufte-book document class which can be modified for other types of LaTeX document:
LaTeX tufte-book.