WordPress MU

Does most standard Wordpress themes work with MU?

Or, there are differences in standard and MU themes?

Technically, in my experience, there's no difference.

In practice, however, you might run into issues maintaining themes that are useful for multiple users. On a single WP install, you can modify things like CSS and header images to suit your needs. On an MU install, changes like this potentially affect multiple users who could be using the theme. Also, depending on the nature of your site, you might like to have a consistent footer, rather than the footer that the theme author has included.

You can download 100 themes that have been tweaked for MU, from < here. I haven't used this pack in a while, but it might be worth looking into.

Has someone ever faced a problem with integrating WordPress theme into WordPress MU?

If so please share what the problem was and how it was fixed (if you managed to fix it)

?

Most regular WP themes can be dropped in WPMU and work just fine. There is no structural difference.

If a theme is not working, you'll have to be more specific. I could honestly write about ten pages of what issues you may run into and how to overcome them. They come from two sources:
- lousy theme coding (including plugin dependencies)
- image thumbnails (vi a plugin)

If you are looking at BuddyPress, that's completely different.