I just upgraded to WP 3 and I've found some buggs with the rebranding plugin.
The first comment on blogs is made twice. First, a comment from Mr Wordpress is made, and then a comment is being made with the content from the rebranding plugin.
Also, the default WP theme says, at the bottom, "This blog is proudly powered by WordPress" (I dont know the exact words as mine is translated). I don't know if that's a bugg or if it's not supposed to be changed with this plugin.
It would also be cool to be able to change the wordpress logo at the top left, before the blogname in the admin panel.