I've got a DOS emulator thingy called ScummVM that I've been using to play
Sam & Max: Hit the RoadI use ZSNES for a couple SNES ROMs (mostly fan translations/re-translations and a mod)...
->Chrono Trigger (Compendium Retranslation)
->Chrono Trigger: Crimson Echoes (beta)
->Der Langrisser, Dragon Quest V (byuu translation)
->Live-A-Live (Aeon Genesis translation 2.0)
->Tecmo Super Bowl III: Final Edition
I use VBA for a variety of games (most of which are on the backburner)...
->Advance Wars
->Breath of Fire II
->Castlevania: Aria of Sorrow
->Dragon Quest Monsters Caravan Heart
->Final Fantasy I & II: Dawn of Souls
->Final Fantasy IV Advance
->Final Fantasy V Advance
->Final Fantasy VI Advance
->Final Fantasy Tactics Advance
->Fire Emblem: Blazing Sword
->Golden Sun
->Grand Theft Auto Advance
->Mario & Luigi: Superstar Saga
->Mother 3
->Phantasy Star Collection (1~3)
->Prince of Persia: The Sands of Time
->Shining Force: Resurrection of the Dark Dragon
->Tactics Ogre: The Knight of Lodis
->Tales of Phantasia
->Yggdra Union: We'll Never Fight Alone
And finally no$gba is the NDS emu i use for...
->Apollo Justice: Ace Attorney
->Bangai-O Spirits
->Castlevania: Order of Ecclesia
->Chrono Trigger
->Disgaea
->Dragon Quest Horoes: Rocket Slime
->Dragon Quest Monsters: Joker
->Etrian Odyssey
->Final Fantasy Crystal Chronicles: Ring of Fates
->Final Fantasy III
->Final Fantasy XII: Revenant Wings
->Final Fantasy Tactics A2: Grimoire of the Rift
->Geometry Wars: Galaxies
->Heroes of Mana
->Kirby Super Star Ultra
->The Legacy of Ys: Books I & II
->Legend of Zelda: Phantom Hourglass
->Lunar: Dragon Song
->Mario & Luigi: Partners In Time
->Megaman Star Force II: Zerker X Ninja
->Megaman ZX
->Meteos
->Metroid Prime: Hunters
->New Super Mario Bros.
->Pokemon Pearl Version
->Puzzle Quest: Challenge of the Warlords
->Resident Evil: Deadly Silence
->Tecmo Bowl Kickoff
->Trauma Center: Under the Knife
->Yu-Gi-Oh! GX: Spirit Caller
No$GBA is awesome if you don't mind lack of window resize capability.
There's a mod for that already, but i never looked into it as that's the least meaningful missing feature (behind numerous bugfixes [forgivable since it's still a current system not counting DSi), save states & fast forward)...