Prefaced with this: It works GREAT on a WP-MultiSite blog :) I had to uninstall and reinstall because my copy had some munged paths, but that was my fault, not the plugin. Caching works as expected, and perfectly.
This was a regular blog magically flipped to Multi-Site, and both sites had Wp-Super-Cache on them.
My 'problem' is in the admin 'layout'.
If I check WP Super Cache from my main blog, I get a note for "Mod Rewrite Rules" saying that "WordPress MU Detected" and I have to update my .htaccess manually. Which I did. And the alert never goes away. Not a deal breaker, but frustrating, since it's pre-formatted and makes the page stretch out.
Then if, as my second blog, if I go to WP Super Cache, I get this: http://yfrog.com/2oscreenshot20100208at8fep
I ended up putting the wp Super Cache .htaccess in both my /public_html folder (where WP 'runs from') and the /public_html/wp folder (where it really is) and that doesn't seem to hurt anything, but it is odd. That made the second error go away, but not the first.
Anyway, just weirdness, but it works so yay. I am a very happy camper.