best emulators for each system (to date)
NES: http://nestopia.sourceforge.net/
SNES: http://snes9x.ipherswipsite.com/
GBA/GBC/GB: http://sourceforge.net/projects/vbam/
N64: http://jabosoft.com/articles/114 (download the 1.6.1 patch and patch the game with it)
PS1: http://www.epsxe.com/
NDS: http://desmume.org/ / http://www.emucr.com/2013/03/desmume-svn-r4559.html (latest build)
(*ps2 and gc/wii require a VERY good cpu. like bare min core i3*)
PS2: http://pcsx2.net/download/development/svn.html
GC/Wii: http://dolphin-emu.org/
Im not really sure how retro you want to go
nes games:
-final fantasy, final fantasy II, final fantasy III (1 and 2 were remade on the gameboy advanced with better graphics, and added ingame content. 3 was remade on the DS)
-zelda/zelda II (zelda 2 was alittle different tho)
-metroid
-megaman series
-mario series
-guardian legend (one of my favs, tho ff/zelda are excluded :P)
-Magic of Scheherazade (a rare title that was really fun, another one of my favs)
-snakes revenge (where metal gear solid began, fun game)
snes games:
(too many to list lmao, here are the top ones)
-final fantasy II (aka IV), III (aka VI), V (they were all remade on GBA, with better graphics and added content. FFII/IV was also remade on the DS)
-zelda link to the past
-Chrono Trigger (really really really good rpg)
-Star Ocean / Tales of Phantasia (both really good Jrpgs, tho they are completely in japanese, tho people have made translated roms)
-secret of mana, som II (another good rpg game)
-starfox
-gradius III
-megaman series
-all the mario games
-super metroid
-castlevania series
-donkey kong series
GB/GBC/GBA:
-FF1-6 remakes (well 3 and 4 may be better on ds), FF tactics advanced
-zelda links awakening DX, zelda oracle of ages and oracle of ages (both are REALLY good zelda games, they were probably the hardest ones made, then them maybe masters quest). zelda minish cap for gba.
-advanced wars/aw2
-golden sun/gs2
-megaman games
-metroid games
-summon night
-castlevania series
-pokemon (ofc)
N64:
-zelda ocarina of time, ocarina of time masters quest, majoras mask
-mario 64, Paper Mario, yoshi story
-Banjo-Kazooie
-Rayman 2 - The Great Escape
-Conker's Bad Fur Day
-F-Zero X
-castlevania series
-Donkey Kong 64
-Star Fox 64
-Goemon's Great Adventure
-Jet Force Gemini
-goldeneye 007 and perfectdark (tho with modern shooting games, they have depreciated, but are still good)
-Star Wars - Rogue Squadron (one of my fav games, tho its extremely hard to get working on emulators)
PS1:
WAAAAAAAAAAY too many to even think about listing lol
ps2/gc also have alot of good games, but idk if you would consider those retro systems, or if you have the cpu to emulate those anyway
And you really cant "play" they games with they keyboard/mouse
so id really recommend a usb controller
somethings like http://www.newegg.com/Product/Product.aspx?Item=N82E16826104402 (which i have an older model of), or usb xbox360 controllers also work pretty well.