Nes : Jnes or Nestopia are both very solid. Jnes is fast, simple and works well with most games, while Nestopia is considerably more advanced with options. For some reason I've mostly played Jnes for it's simple approach.
http://jabosoft.com/index.php?categoryid=1
http://nestopia.sourceforge.net/
Snes : Zsnes is my personal favorite Snes emulator, but Snes9x is good too so it comes down to personal preference
http://www.zsnes.com/
http://www.snes9x.com/
N64: Project 64 is hands down the best emulator for N64. I myself have never found a game it won't play to near perfection.
http://www.pj64-emu.com/
Gamecube/Wii : Dolphin is a great emulator that works for both Gamecube and Wii (I play several Wii games without lag or glitches, and I got through Twilight Princess and Windwaker without lag or problems on gamecube). There is a bit of a setup involved but with patience it'll go so long as your computer can handle it.
http://dolphin-emulator.com/
Gameboy : Visualboy Advance definitely for Gameboy.
http://vba.ngemu.com/
Nintendo DS : Last I checked it out the DS scene was a work in progress, however iDeaS was far and away the best emulator and I suspect it still is. I was able to play some Castlevania games on it but I didn't spend enough time to say you can complete them.
http://www.ndsemulator.com/nintendo-ds/ideas.htm
Playstation 1 : Epsxe is a GREAT Playstation 1 emulator, however there is another emulator simply called "psx emulator" that is extremely basic and extremely accurate so if you want to avoid technical shit and having to get the plugins it's as good an emulator as any, and if you don't want the BS of setting another emulator up it's definitely the way to go. Playstation emulators are by far the hardest ones to set up, with a lot of third party plugins required to get the most out of it. If you do go with Epsxe (the true winner here) I can help you get the best plugins for improved graphics/sound and such I've got it all set up for awesomeness.
http://www.epsxe.com/download.php
http://psxemulator.gazaxian.com/
Playstation 2 : PCSX2 is THE Playstation 2 emulator, I got through Xenosaga series without too much trouble on it, and the first Xenosaga is notorious for being hard to emulate. Again as with PS1 this can be a bitch to setup although I have not tried to newly released v1.0 so it might be streamlined by now. This emulator WILL kill your CPU resources, PS2 is much harder on resources than Gamecube or Wii.
http://pcsx2.net/
Genesis/Gamegear : Gens or Fusion. I prefer Gens personally, and if I recall they also support Gamegear games.
http://www.gens.me/
http://www.eidolons-inn.net/tiki-index.php?page=Kega
Dreamcast : I personally found Dreamcast was never given a great emulator, but Chankast will get you through many of its games.
http://www.chanka.org/
Sega Saturn : I hope you don't want to play Sega Saturn games because its emulation scene is shit.
That about sums up my Emulation knowledge, but I think you'll find it accurate. I have played a LOT of emulators over the years, almost all of them, I started way back when emulation was in its infancy and I've loved it ever since.
