All the below is testing on a New 3DS. On original 3DS, assume lesser speeds.
Virtual Boy performance is fairly unplayable, expect about 15FPS (one quarter speed). There's no 3D support in the sense that you'd expect it on a 3DS, but you can play in anaglyph mode with some old red/green glasses if you want.
WonderSwan performance seems great, but RetroArch is still not really equipped to handle the WonderSwan's control scheme when it comes to vertical titles or games that alternate like Klonoa. The original console was intended to be physically rotated in your hands, meaning your fingers were now on a bunch of buttons that they weren't on before. RetroArch doesn't know what the deal is with this. If you want to play exclusively horizontal games, you're fine; if you want to play any vertical games, you'll need to adjust your controls; if you want to play any games where rotation is necessary, just give up, you'll have to change the controls every time you rotate and you will have no fun. (Sorry to be a downer here; again, the actual performance is great. WonderSwan just doesn't fit well into the RetroArch design.)
Neo Geo Pocket/Color performance is about 45FPS, or three quarters of full speed. If you're committed to playing NGP/C games, they're certainly playable at this speed, but you know: 3/4 as fun as they should be.
You didn't ask, but Sega CD performance is also fairly playable. In a game like BC Racers which uses the Sega CD CPU relatively heavily, you get around 55 to 60FPS in gameplay (the FMV sequence on startup runs like crap, but doesn't matter much in terms of enjoying the game). You could probably play PAL versions of games like this at full speed (50FPS), but keep in mind the 3DS screen has no 50Hz support, so you may not like how the 50FPS display looks on a 60Hz screen. You also might not notice it at all. Secondly, I didn't test Sonic CD, but I would speculate that it probably runs quite well (maybe even 60FPS), as it barely uses the Sega CD hardware except as a CD player. It's pretty much a stock Mega Drive game. This is probably true for most Sega CD games which are enhanced versions of Mega Drive titles, like Earthworm Jim and that one Spider-Man game.
You also didn't ask about Virtua Racing for Mega Drive (for those out of the loop, this game had an on-cartridge processor, like the Super FX in Star Fox SNES), but this performs quite slow, hovering around 35FPS. It's fair to point out, though, that this game was insanely fast on the Mega Drive. It's a much easier game running at just over half speed. Somebody might even enjoy it more like this. But it's very slow relative to the original, regardless.
