AC Toolbox
Audacity
Ardour
Csound
Cubase (and License Control Center)
Final Cut (or FC Express)
Finale
JackOSX (and QjackCtll)
JackTrip
Ableton Live!
Max/MSP
Melodyn (plugin)
PureData (Pd-extended)
Reason
Sibelius
Spear
SuperCollider

Secondary (found in Applications folder):

Cecilia
Ceres3
CLAM (QtSMStools, NetworkEditor, Prototyper, Annotator,Voice2MIDI)
Chuck and MiniAudicle
Common Music
JAMin
MIDIKeys
Praat
PVCX
sndtools (sndpeek, rt-pvc, rt-lpc)
SooperLooper
SoxWrap
Tapestrea

Plugins and externals:
This section is to be expanded

Additional (non-music):

Auqua Emacs
Firefox
ffmpegX
GIMP
Handbrake
MPEG Streamclip
iMovie
Inkscape
NeoOffice
Scribus
Smultron
Transmission
Cyberduck
VLC

System Utilities:

Perian (for extra video formats)
Growl
DoubleCommand
Flip4Mac (for wmv/wma format support)
Quicksilver
The Unarchiver (for Stuffits support)

Drivers required:

Apogee Drivers
RME Fireface drivers
M-Audio drivers