I remember experiencing that once, after a game crashing (I was messing around with custom graphics on Smash Bros Brawl). It was like a slight slowdown that affected THE ENTIRE SYSTEM.
I really don't know if it's the same problem that you have, but what I did, once I noticed it happening, was... Well, first, panic.
After that I restarted the system a few times, (turned it on, went to the main Wii menu, see if it was in slowdown, if yes, I turned it off and back to the first step). After three or so attempts It went back to normal, and it never happened to me again. I also stopped messing with custom graphics just to avoid that happening once more.
Sorry for not having more info...