We've heard from a number of people that YouTube has recently blocked a number of fanvids due to alleged music rights violations. But YouTube also provides a mechanism for vidders to assert their right to fair use: a quick and easy dispute process.
YouTube recognizes that there are legitimate artistic and critical reasons to use copyrighted material, and the online form gives, as a potential reason for dispute: "This video uses copyrighted material in a manner that does not require approval of the copyright holder. It is a fair use under copyright law." The form also asks you to explain further.