If you're on a Mac, then MPEG streamclip works fine. You can find it here
http://www.squared5.com/ . I've used it to transform Youtube flv format to mp4, but from memory you first need to install the Perian library, available from
http://perian.org/ .
I must add, if you're downloading Youtube flv/swf files, now days there's an easier way. Firefox has a plug-in called "downloadhelper" which automatically converts Youtube flv/swf files to mp4.
