By default, WordPress MU runs all of your posts through an HTML filter - stripping out any tags and attributes that it deems insecure, so say good-bye to iframes, inline JavaScript, and Flash embeds. This would be fine if it were configurable, but sadly it is not. Various hacks exist to remedy the situation, but for such a pluggable piece of software as WordPress - hacks just seem too much like... hacks.
Enter the Unfiltered MU plugin.
Unfiltered removes the HTML restrictions imposed by a default install of WPMU, allowing you to post whatever content you see fit. It can be set up to turn off HTML filtering globally or on a per blog basis.