Use FBI to install CIAs of these. These each have their own thread here on this forum.
Bubble's versions of these emulators are pretty good and run fast even on o3DS:
TemperPCE (PC Engine)
Snes9x
VirtuNES
Picodrive (Master System, Gens/Mega Drive, CD / 32x)
Gameyob DSi version for GB/C games at native resolution, mGBA for the same if you want to scale them.
See the Super Injector thread on this forum if you want to do Virtual Console injections for S/NES, GB/C/A. GBA injects in particular run semi-natively and much faster/more compatible than the best emulator, mGBA. The SNES emulator is also more accurate than other options and generally fullspeed. 8-bit emus are good enough that its hard to tell between them and VC, and the NES VC is missing many mappers.
I think there is a half-decent SCUMM port for old Lucasarts games and the like, and handy is about perfect if you remember the Lynx handheld..
You can use Retroarch for the remaining. In particular FBA NeoGeo runs about perfect on N3DS, and Genesis GX plus is good for game gear.