I always love going back and playing Star Fox again but several emulators have trouble with the FX chip games so they sometimes run slow.
Super Metroid, Chrono Trigger, any of the Donky Kongs, EarthBound, any of the Megaman games, Pilot Wings, Top Gear, Turn and Burn: No Fly Zone, Wings 2: Aces High, Wolfenstein 3D, Zombies Ate My Neighbors
Obviously any and all of the good Mario games (you might even want to try out the offputting but interesting Mario is Missing or Mario’s Time Machine.
As for gameboy definitely get Super Mario Land, that game is timeless. The DX version of Link’s Awakening and the Oracle of Ages. Obviously you can’t forget Pokemon, can’t think gameboy without bringing that up.
I always used snes9x for my emulator needs, but recently I’ve been using one made for PSP. It’s nice having my entire videogame childhood in my pocket.