Emulators I use fairly regularly:
JenesisDS - Very nice Genesis emulator, has worked with everything I've tried except Sonic 3 & Knuckles. Has the nicest interface of any of the emulators I've tried, something that is definitely neglected by most of these.
LameboyDS - Game Boy (Color) emulator, was inferior to Goomba Color on the GBA until the two most recent releases, now it runs everything Goomba does and faster in a few cases.
nesDS - Inferior to PocketNES but you might want to take a look at it anyway, it has nicer scaling but doesn't remember any of your settings and doesn't work with as many games.
PocketNES - This is for the GBA, make sure you get the menu maker because it can't read ROMs from your card, they need to be merged into pocketnes.gba, that's what the menu maker does. This is far more accurate than nesDS and is updated fairly regularly.
SNEmulDS - SNES emulator, grab version 0.6. Not many games are enjoyable with this unfortunately because of how layering is done, you'll get into a game and then find you can't kill a boss because it's completely invisible or something. Does work great with a handful of games though, BS Zelda is nearly perfect on it.
If you want any other systems they probably exist, check
here.
For homebrew:
DSOrganize - Seems fairly popular, I've never had much use for it but you might.
Colors! - Fun drawing application, even if you're not interested check the gallery, you won't believe what some people can do with this.
QuakeDS - Awesome ports of Quake and Quake II, if you like those games be sure to get these.
