A good site to start with is http://www.emucr.com/ . They have the most recent builds, almost daily, of PCSX2, PCSXr, Dolphin, and many others.
Playstation 2 - PCSX2. Speed is still an issue for them, but it gets regular updates. So far it's the best and most complete one
Gamecube - Dolphin. Believe it or not, Gamecube emulation is almost perfect. Also regularly updated, this one is coming along.
Playstation - PCSX Reloaded or PSx. PSx is older, but many games work perfectly with it, while PCSX Reloaded is actively worked on. (It's an outside continuation of PCSX) Some games work better in one than the other.
Dreamcast - NullDC or Makaron. Dreamcast emulation is almost perfect now. Both Makaron and NullDC are actively worked on, the only issue is that games that require WinCE won't run right. (Not many require this.) Demul is coming along, but so far NullDC is the best one.
Saturn - This is tricky, as the Saturn is a pretty hard machine to emulate. There are some out there, but none really work well enough to enjoy playing anything yet.
Jaguar - Same deal. Some are out there, but nothing really playable.
3DO - Ditto.
Genesis - I use Kega Fusion. It's by Steve Snake, and emulates pretty much every Sega 8 and 16 bit system. (Even Sega CD and 32X games)
Super Nintendo - BSNES. Not Snes9x, or Zsnes. BSNES. This is a newer emu, and the author has gone completely for accuracy. It is now easily the best SNES emu out there. (It even runs FX games perfectly.)
PC Engine/TurboGrafix/TurboDuo - I use Magic Engine. It's older, and the full version actually costs money, so I really won't recommend it. Here's a place to find other ones -
NES - Nestopia. It supports the most mappers and seems to be the most accurate that I've seen. There may be better ones out there...
Sega Master System - Kega Fusion. See Genesis, above.
Nintendo GB/GBA/DS - Just get WinDS Pro. It's a collection of 4 or 5 emus for the Nintendo handhelds, and is updated pretty regularly. I use VBA for GB/GBA titles and NO$ for the DS stuff. The main site is not in english, but it's pretty easy to figure out.
Apple 2 - AppleWin. The latest build can usually be found in the Emulators directory on Asimov.
C64 - I use WinVICE. It works really well. There may be a better one though, I'm not sure...
Amiga - WinUAE. This is almost perfect, and is easily the best Amiga emu out there.
Atari 2600 - Stella. The author can actually be found here on this forum, and it is actively worked on.
Atari 5200 - If you want just a 5200 Emu, Kat5200. Others are good for 5200/800 emulation.
Others - http://www.zophar.net/a5200.html
Atari 7800 - Emu7800. Does the job, for the most part.
That's all I'm listing for now. These are pretty much the ones I use. I stuck to console and computer ones, and left out the arcade ones, like MAME, and the NAOMI board emus. Feel free to help out, anyone, and I hope this helps out a little to those that are not up-to-date or are flat out new to emulation.
Edited by HuckleCat, Fri Aug 6, 2010 10:28 AM.