VC emulation for NES & SNES is perfect, there is a slight blur implimented in order to replicate the quasi anti alasing that you get from a CRT (Since the games were designed to be played on such displays, they were not visually designed to be completely sans filters. Hence adding a very slight blur is actually a more accurate way of preserving the original image on a modern TV)
Also, AFAIK Nintendo's VC emulator is the only one to have accurately emulated Kirby Dream Land 3's psuedo high resolution mode for its transparancy effects (Just to sight one example)
MD emulation is also spot on with it being the only commercial emulator to emulate the Mega Drive sound chip accurately. It also emulates without any filters, which matches the original MD's video output, which was crisper than the NES and SNES.
The TG16 emulator is not as accurate since is it is too blurry for the older VC games (They haven't been updated with the newer TG emulator, which was used from Ys 1& 2 onwards and runs without filters)
So far NeoGeo (What little of them has been released anyway :lol) is also completely accurate, as is the Master System.
N64 emulation is technically not done accurately since it uses HLE, but this is a much better choice for this console because the games look and run much better than on the original machine! (Not to mention that the GCN controler is way better than the original N64 one with its now broken analog sticks
) For all intents and purposes, the emulation is graphically and audibly accurate (Apart from some extremely minor audio skips at a few loading points in some games)
The only VC emulator which isn't really 100% accurate is the C64 emulator, as some games have been reported to contain a number of emulation glitches (At least in Europe, so far I don't think any have been reported in the US versions)
The reason why VC emulation can be 100% accurate is because they have seperate emulators for each game, so they can tailor the base emulator to work perfectly with that one single game. PC emulators will never be 100% accurate because they are designed to run every game in one emulator. Unfortunately, Backbone love to take the lazy route and just slap the ROMs in a single base emulator for all of their releases, that isn't tailored to the games they are using with it.
It also helps that Nintendo just happen to know how their own hardware works!