if your film is a 'documentary'or it is for research, educational usages, or it has less than 10% of the finished film that contain copyright material, you can 'get away' under fair-use
BUT, you still is liable to be sued and you must go to court to prove to the court that you were doing it under fair-use clause.
So... Anything that is copyrighted or trademarked, you MUST get permission, some people said parody/comedy 'CAN' get away it, but not really...
I did a parody fan film so kinda digged a lot into copyright concerns, plus recently I was approached by a fellow about shooting his feature that has a lot of political and corporate names in it, plus pictures, etc. after consulting with my entertainment attorney, she said I have 60% chance of being sued, and it might tarnish my reputation, I have to think twice on it...
So, ask them, you have nothing to lose, I once emailed Sigur Ros and asked to use their song and music video, and within 24 hours, I got a yes, sure for a short film of mine.
Also keep in mind, MOST film festival would not be that interested in any films that have copyright material in it, just because they may liable to be sued as well. Distribution wise, you need clearance so again, something to think hard about...
Best of all, ask them, or consult an entertainment attorney (or a bunch, make sure they also understand intellectual property law), make sure you REALLY provide the information so they wouldn't give you wrong advise (this happens a lot).
Johnny Wu