Software

• Aquamacs — Finally, a version of Emacs native to Mac OS X.
• Colloquy — IRC client for OS X.
• Delicious Library — Fantastic program for keeping track of your books, music and movies.
• Dropbox — Amazing file sync utility.
• ecto — Blogging client for Mac OS X.
• FBReader — E-book reader for Linux desktops and PDAs and, most importantly, the Nokia 770.
• Fetch — Venerable FTP client which supports Kerberos sessions.
• Firefox — The best open source browser around.
• Flip4Mac WMV — Windows Media components for QuickTime.
• Gimp — The GNU Image Manipulation Program. Now available as a Mac app.
• Google Earth — Amazing.
• GPG Tools — Tool for encrypting/decrypting with GPG; useful if, like me, you can’t get GPGDropThing to work.
• Growl — Very nice notification system for OS X.
• GutenMark — A handy tool for automatically generating HTML and LaTeX markup from plain text e-books, like those found on Project Gutenberg.
• Inkscape — Open source vector graphics editor. The free alternative to Illustrator.
• iWork — Because Microsoft Office is garbage and OpenOffice is a cheap knockoff of garbage.
• LaTeXiT — LaTeX utility for quick equation typesetting.
• Macaulay 2 — Free computer algebra package geared towards algebraic geometry and commutative algebra.
• MacFusion — GUI interface for the Mac port of the FUSE framework, which allows you to access filesystems you might ordinarily access via FTP or SSH directly in the Finder.
• Mac GPG — GnuPG encryption for OS X.
• MenuCalendarClock — Useful menubar calendar.
• Mira — Use your Apple Remote to control more than just Front Row.
• NetNewsWire — The gold standard for RSS readers in OS X.
• OmniOutliner — A fantastic program for creating lists and outlines.
• Papers — PDF manager with a specific emphasis on scientific papers.
• Pathway — Visual, network representation of your meanderings through Wikipedia.
• Perian — Enables QuickTime support for many other video codecs.
• Pukka — Nifty Delicious client.
• Quicksilver — Launcher and framework for OS X.
• Skim — PDF reader with built in annotation and "snapshot" capabilities which plays well with LaTeX’s PDFSync.
• Skype — Free video calls made easy.
• SuperDuper! — Fantastic backup software for OS X.
• TestXSLT — Handy Cocoa application for testing XSL transformations.
• TeXniscope — Nice PDF/PS/DVI viewer for Mac OS X that supports LaTeX’s PDFSync.
• TextMate — Remarkable text editor for OS X; this is my current text editor of choice.
• TextWrangler — Free, capable text editor from the makers of BBEdit. I use TextWrangler for very large files, which it handles much better than does TextMate.
• Transmit — OS X FTP client.
• Twitterific — Standalone Twitter client for OS X.
• VLC — Highly capable media player.
• VoodooPad — Wiki-like notepad which is fantastic for keeping track of lists, notes, ideas and deadlines.
• Xee — Image viewer for OS X with more functions than Preview.

Web

• Beanstalk — Simple Subversion hosting.
• Delicious — Popular social bookmarking site. Check out shonk’s Delicious page.
• Flickr — Photo management. See my photostream.
• Google Scholar — The Google magic applied to academia.
• Instapaper — Your personal list of links to read later.
• Markdown — An extremely nice text-to-HTML formatting syntax, used for most of the content on selling waves.
• Oxford English Dictionary — The best dictionary on Earth.
• Ta-da List — Well-designed, easy to-do lists.
• W3Schools Web Tutorials — The ultimate resource for anything web-related.
• Wayback Machine — See what information a web page used to contain before it was edited or deleted.
• Wikipedia — The free online encyclopedia.

Safari hacks

Note: At one time or another I used all of these fairly regularly, but the only one that’s still installed on my system is Inquisitor.

• DownloadComment — Automatically adds its source URL to the Spotlight comment for each file you download.
• GrowlSafari — Add Growl notifications to Safari.
• Inquisitor — Spotlight for the web.
• Pimp My Safari — A repository of Safari hacks.
• SafariBlock — AdBlock for Safari.
• Safari Enhancer — Turns on the Debug menu and other enhancements.
• SafariPlus — Essential plugin for per-site cookie management.
• SafariStand — Multifeatured plugin that adds a lot of functionality
• SurfRabbit — Customize how virtually any page is displayed.

Firefox extensions, themes and tools

Note: I don’t really use Firefox much anymore, so many of these are probably out of date.

• About Site — Adds context menu providing information about the web site you’re viewing.
• AJAX Yahoo! Mail — Uses AJAX goodness to make Yahoo! Mail more useful and Gmail-like.
• BugMeNot — Bypass web registration.
• CopyAllURLs — Copies the URLs of all tabs into plaintext, HTML, or custom formats. To make the STX option output Markdown syntax, replace the standard copyallurls.jar file with this one.
• Dictionary tooltip — Displays the definition of a selected word in a pop-up menu
• foXpose — Creates an Expose-like pane of all your tabs for easy switching.
• Greasemonkey — Add DHTML to any web page.
• iFox — Simple, clean Firefox theme that borrows from Safari.
• Linkification — Converts plain text URLs and email addresses into links.
• Menu Editor — Edit any and all of the menus in Firefox.
• Mouse Gestures — Adds mouse gesture functionality
• OpenNewWindowFromHere — Duplicates the current window in a new tab or window.
• Optimized Firefox Builds for G4, G5 and Intel Macs.
• PPC Optimized Firefox builds — Optimized to get the best performance possible for Macs.
• Redirect Remover — Removes relinking URLs from web links.
• Tab Mix Plus — The ultimate tabbed browsing extension.
• Tab Preview — Generates a scalable preview of any tab.
• TinyURL Creator — Automated TinyURL generation.
• Zotero — Sophisticated Research tool.

Movable Type plugins

Note: The main blog is now powered by WordPress, not Movable Type, so you’ll probably only see these being used in the older archives. For a list of WordPress plugins used, see below.

• Markdown — A text-to-HTML converter that renders an easy-to-read syntax into valid XHTML. Used to format all posts.
• MTAmazon — Uses Amazon’s API interface to retrieve and display products. Used on the books page.
• MT-Blacklist — Useful tool for blocking and cleaning up comment spam. Used wherever you see comments.
• MT-Refsearch — Technically a hack, not a plugin, this allows me to direct readers who land on the front page from search engines to posts containing their search terms.
• Regex — Allows search and replace in templates using regular expressions. Used in the main index and archive templates to render entry URLs without the trailing .php.
• ShortTitle — Retrieves a “short title” from the keywords field of an entry. Used to make entry URLs less ungainly and to retrieve URLs for the linklog.
• SimpleComments — Presents comments and trackbacks in a single list. Used wherever you see comments.
• SmartyPants — Translates plain ASCII characters into correct typographical HTML entities. Used in conjunction with Markdown to format all posts.
• Textile — Another text-to-HTML convertor. Formerly used to format all posts, since replaced by Markdown.
• Word Count — Counts the number of words in an entry. Used in the excerpts feed to provide a word count along with the post summary.

WordPress plugins

• Akismet — Comment Spam killer.
• FeedList — Enables republishing RSS and ATOM feeds through WordPress. Used for the linklist on the main page.
• Miniblog — As the name suggests, creates a miniblog useful for asides, linklogs, etc. Used for the quote of the day feature at the top of the main page.
• PHP Markdown — A PHP port of John Gruber’s Markdown text-to-HTML converter. Used to format all posts.
• Weighted Words — Creates a list of the most commonly-used words on your WordPress blog scaled proportional to frequency. Used to create the zeitgeist at the bottom of the main page.