I put my list of applications in a spreadsheet and rated each one on usefulness. I didn't include the stock apps like Iphoto, which are indispensable, or Microsoft Office, a necessary evil. Here is the list, with a few comments.

• Dropbox: sync your files among multiple machines seamlessly


• Openoffice.org: A free version of Word. Feels a wee bit sluggish, and I prefer Iwork.
  


• Terminal: learning a few simple commands, like how to kill hung programs, or copy everything on your desktop into a folder, has saved me hours and hours of tedium.
  


• VLC: watch any video format


• HandBrake: convert dvds to Ipod format


• Jomic: comic viewer


• Jumpcut: Copy something. Copy something else. Go back and paste the first thing you copied. Awesome.


• KompoZer:
  Free web page creation tool. I use this instead of Dreamweaver because I hate how Adobe products install extra gunk all over your machine and eat up resources. It has some minor bugs but no dealbreakers.


• MacTheRipper: Copies DVDs to your hard drive for later viewing on the plane.
  


• Tex-Edit Plus 4.9.8: I've been using this for over a decade. Great for cleaning up mangled email and other texts. Has a great command called "copy lines containing" so you can copy every line with a particular phrase in it, for example.
  


• Textwrangler: snappier than Tex-edit, better with large files, but a little harder to use.
  


• Gimp: Basically, it's photoshop, and it's free.
  


• Audacity audio editor and mixer
  


• Colloquy: Irc client. I've heard you can use #bookz to find e-text versions of books you own for the aforementioned plane flight.
  


• Cyberduck: ftp client. Honestly, I just use the command line in Terminal.
  


• Notational Velocity: Nifty, no frills note-taking app with lots of keystroke commands. Syncs with the Iphone app simplenote.
  


• RapidWeaver: Relatively cheap alternative to Dreamweaver. Bazillions of templates and plugins.
  


• Zoom: For playing those old text adventure games.
  


• Vitamin-R: Task reminder tool. You may not need this. I do. Slightly buggy.
  


• Amazon MP3 Downloader: Amazon throws up free music all the time, and some of it is good.
  


• FreeMind: One of many mind mapping tools. I like Graphviz too, but haven't used it lately.
• Anki is an intelligent flash card system that quizzes you on content that you are on the verge of forgetting. Basically a free version of the popular Supermemo.