VC is the most accurate IF it supports the chips for your game at all. NES can be a bit spotty there, and of course no super FX. Also a mild dimming effect that I'm not a fan of.
However Bubble's emulators all run cart games at full speed, even on o3DS, so speed isn't an issue. There tend to be some minor audio or visual glitches with various games but its pretty good.
GBA VC is a special case since it is more like running a DS game. Accuracy, compatability and speed are near perfect and other emulators cannot approach it, but you won't have save states.