Testing SuperCache 0.9.9.2 in WP 3.0-RC3 in MultiSite mode, it seems to be working fine (so far, only tested on one site) but I keep getting a message on both the pages Super Admin > WP Super Cache and Settings > WP Super Cache (is there any difference between the two anyway?) :
A difference between the rules in your .htaccess file and the plugin rewrite rules has been found. This could be simple whitespace differences but you should compare the rules in the file with those below as soon as possible. Click the ’Update Mod_Rewrite Rules’ button to update the rules.
I checked both .htaccess files and copy pasted the rules again to be sure but the message remains.