I have Cool Edit and Sound Forge - SF wins hands down. It is much more flexible for editing Wave files - I've used it to transfer a vinyl album with a big scratch onto my hard drive, then carefully pencilled out the scratch...

For MIDI I'm still using Cakewalk 3 - the newer versions just don't seem as solid or intuitive.

For actual printed music, Noteworthy is one of the best - Cakewalk has some idiotic quirks like insisting on Bb when the context demands A#, for example. It also insists on making the odd bar which is a little 'busy' spread the width of the page - but it's great for MIDI.

I prefer sorting out the MIDI in Cakewalk, then using Noteworthy to print out the dots.