Frequently used free apps, in alphabetical order:
Address Book: Apple's native contacts app. I use it with Quicksilver and sync it to my iPod Touch.
Adium: Very nice, customizable IM client. Allows me to run MSN, GTalk, and FaceBook. Too bad there's no video chat...yet. For that, I have the new Google plugin, iChat, and Skype anyway.
Alarm Clock: A simple, but pretty powerful alarm app.
Convert Pictures: Useful automator functions for converting images into different formats without having to go through Preview or Photoshop manually.
DisApPear: Hides and password protects folders.
ffmpegX: Powerful video converter.
Firefox: Not entirely happy with Firefox...but I prefer it over Safari and Camino. Maybe I should try Opera. I like the plug-ins though.
FormulaPro: To type on pdfs. I can use Adobe Acrobat 8 for this, but FP is lighter.
GimmeSomeTune: iTunes companion app. It's a GrowlTunes replacement and it fetches and displays lyrics, album art, etc. Excellent app.
Grand Perspective: Tells me where all my hard disk space has gone.
Growl: Used with Adium and Mail.
Handbrake: Rips DVDs into video files (as opposed to Video_TS folders)
Image Tricks: I use this to quickly crop images.
iSquint: Converts videos. Lighter and sometimes better than ffmpegX. It's not open source and needs compiling. I forget what the new name is.
iStrip: Comic strip reader. A little buggy, but it works.
iTunes: Der. With ****loads of scripts.
Mac the Ripper: Very powerful DVD ripper. Rips into Video_TS folders.
Mail: Mail client. Came with the Mac.
Max: CD ripper and audio converter.
Preview: New Preview is powerful enough to replace some of my older apps (e.g., PDFLab). It's now a great tool for image/pdf viewing and manipulation.
Quicksilver (esp. with Calculator, Dictionary): This is a HUGE reason for why I love Mac OS X. I'm not even going to describe it. Get it. Now.
RapidoResizer: Quickly resize images.
Renamer4Mac: Quickly batch rename stuff.
Skim: Powerful PDF reader/notation-thing.
Stuffit Expander: Unzips and stuff.
Vienna: RSS reader. I prefer this over NetNewsWire and...what was that other one that was recently made free? Not sure why.
VLC: Video player. Is awesome.