NESticle and KGen have been good for me respectively, though your mileage may vary. If you still want to maintain some semblance of a productive life, stay away from the arcade emulators (MAME, Callus, etc.).
Thanks AS, I've had an itching for some Donkey Kong Jr. the past few days and I'm going to spend this weekend scratching.
Oh crap, let's see if I remember which ones I have. NES - Get JNES. Some people praise NESticle, but a couple of games for it have problems, most notably in Mike Tyson's Punch Out. Kid Niki doesn't even work on NESticle. Never had any problems with JNES SNES: ZSNES - Easy to navigate menus, and they finally fixed the layering bug that used to plague this emulator. Genesis: GenX - THe only problem with this one is that I can't save my custom guy in NBA Hangtime. I'm not sure if this is a bug with that ROM or with the emulator I also have a Sega Master System, Turbo Grafx 16, and Atari 2600 emulators (Pitfall rules!), but I haven't played those in a long time...
For Sega Genesis I use Gens. Kgen doesn't work for me. I dont know if it is because I'm running Windows XP or not. But I have no problem with Gens. For NES I use JNES. It's the only one I've you for the NES but it's one of the best imo. For SNES I use ZSNES or SNES9x. Let me recommend a game for Genesis. Landstalker. It's the best game I've played for Sega. To play it easier you will need a Sidewinder d-pad (one that mimics the sega controller but has L and R triggers). The reason is because of moving with the character is a little hard with the keyboard but you will get use to it over time.
I never realized the power of the emulators before. I thought they were just used to play the game. A while back, I finally looked at all the features in ZNES, and then I was able to pretty much set it up so that I could gain 50-60 levels in Chrono Trigger in the beginning without playing. Plus, if I died, I could just cheat and go back 5 seconds before I died. I think I made it like 4 or 5 levels in Contra without dieing once, cheating of course. Wish there was a button on my PS2 that could let me go back 5 seconds after giving up a 70 yard TD.