Its taken me a year to settle on my favorites.
Note: Some of these may not be Universal Binary.

Spark = Hotkeys, Visit Website
Quicksilver = Launching stuff, Visit Website
Disk Inventory X = File Management, Visit Website
Genius = Study tool, Visit Website
Wallet = Password storage, Visit Website
Miro = Internet TV, Visit Website
URLwell = Commonly used url’s storing menubar app, Visit Website
VLC = Best video player hands down, Visit Website
X-Chat Aqua = IRC app (on-join+perform), Visit
CyberDuck = FTP app, Visit
Blender3d = 3D graphics, Visit

Favorite Mac App websites:
http://www.freemacware.com
http://www.versiontracker.com