I probably use at least a dozen of the .apps promoted in this thread. I've also probably contributed in the past, but I can't be sure if it was this one or another. Either way, these might be repeats...
Dockless allows for running applications to be removed from the Dock entirely. This program is perfect for people who like a super-clean dock but multiple programs running in the background. I use(d) it for
MenuShade and
Stattoo, among others.
The only mac os x souulseek client I could ever get to work properly,
s o u l s e e X.
I use VLC, Quicksilver, Adium, SuperDuper, UnRar, X, and Speed Download as well. Those are pretty standard, though, as maybe half or more of this community seems to use those.
Also, I wouldn't link it here because some may say it's used for illegal intentions (although I did already link ssX, so maybe I'm just a hypocrite...) but Senuti is great for those who use their iPods as external hard drives/thumb drives.
I'm a big menubar fan, so
Mail Status Control,
iRun,
Ejector,
LogMeIn (while not a true "program," it is still a great tool), and finally
EasyWMA, because for some reason the Windows version of iTunes converts .wma files but the Mac OS version cannot.