Nero, Codec Pack, MSN + mess.be patch, Firefox + add-ons, Daemon, iTunes, Winamp, uTorrent, Joost. Others also, but those are what get put on right away after a fresh format/re-installation.
Besides the normal browser, mail, media players, etc: I would cease to function without adium, coda, newsfire, quicksilver, photoshop, and most recently logic express. I need iwork and mathematica for school. Basically, I'm apple's bitch.
Firefox with addons (if it didn't have the addons, I would cry, so I back them up ) Office 2007 (Ultimate, free & legal) Synergy - so useful for controlling 2 computers A media player (foobar or iTunes, I only just made the switch) VLC & WM Classic Daemon tools Speedfan or other monitoring software Steinberg Wavelab (sound editing)
Amarok (Winamp sucks, IMHO. So does iTunes and WMP. Foobar's okay, but takes to long to setup) Firefox VLC Daemon Tools
ok, in no order: firefox, itunes, azureus, photoshop, counter strike (but not played it in ages), Adobe reader ( i read so many pdf files), sonic recordnow ( its so easy to use, plus i got it for free ) oops forgot msn aswell
mctigger: For just reading pdf's, you might want to use Foxit instead. It's free and a LOT less bloated than Adobe's reader.