Firefox + extensions like foxytunes, adblock, flashblock, Cookie editor, FireFTP. Having played with opera I would also consider that a fine replacement.
Offline list, my favourite way of sorting Roms. Emulators for said roms too.
Any and all windows tweakers I can lay my hands on (browse around freeware/shareware sites for these).
MP3 tag, able to sort my music collection (supports just about every music container known to man).
Graphics programs, pick your poison here.
Video programs, I could reel off an insanely long list here but AVISynth +Plugins (deinterlacers (DGBob my favourite for this), sharpening/noise removal tools etc), VirtualDub, DGIndex, Ifoedit, DVDShrink, DVD decrypter (now have a look at RIPit4me too), PCGEdit (comes as part of the ripit4me package), CCCP (combined community codec pack: the only codec pack I trust, comes with my favourite media player: media player classic) and an MPEG2 encoder (HCEnc, QuEnc or CCE are my choice although there are others), GSPot (used all the time for codec detection and errors). Next time I will include megui too as having played around with it for a while now it is fantastic.
An office program, I like MSOffice but OpenOffice works for me too.
Zone Alarm, there are better but this one works for me.
Usenet/Torrent programs. I do not use either really anymore but for the odd occasion Newsleecher and μtorrent.
Trillian, does all the instant messaging I care about with all the functionality I care for and has a free version.