As a owner of both 9.2 above and below firmware o3ds' I can say most emulators run very well in user mode (3dsx), even just as well as the .cia builds. The only things that are better on kernel mode is pcsx (barely but what do you want its new), gpsp, and picodrive (and thats only for 32x stuff) because of the dynamic recompiler. Even Picodrive is amazing on user mode.
The emulators to stay away from regardless of what o3ds you have is the neogeo pocket, wonderswan, catsfc/plus, snes9xnext, nestopia, fceumm, mGBA, CPS1, CPS2, and PCSX. Right now those emulators are so slow, or just come up short imo I can't run an emulator unless it has at least full speed I can deal with no sound.
There's also pokemini, handy3ds (Though those are kinda buggy), GameYob, and blargsnes that aren't retroarch ports that rock regardless of O3DS FW.