Hmm, on a tube TV there really is no lag from VC, so maybe it's just something in the game itself that you're not accustomed to. I've been playing a lot of early NES games, like Double Dragon, and I'm very sensitive to minute timing issues, so I'd notice if there was even a slight problem.
Now, Kirby's Adventure does slow down when there are too many enemies on the screen at once, but even then there hasn't been an input lag, just a general slowdown.
I see that mentioned SMW specifically, but I've been playing that one off and on as well and have been happy to see that there isn't any lag (I used to play that game on emulators and the slight lag drove me crazy). Out of curiosity, which controller have you been using, Classic or GC?