Fanart always gets a bad rap, I hear mixed things about its professionalism.
Is it bad form to put uncommissioned fanart in your portfolio, even if its a well done, finished piece you would put in there otherwise?
I've done a lot of fan art, some of it I'm very pleased with, but I'm always hesitant to put it in my portfolio.
I highly recommend against it unless the company you are applying for isn't into creator-owned work. I think DC and Marvel are somewhat okay with this. The only complaint I've heard as far as those is the portfolios where all of the characters drawn have their masks on, when the editors want to be able to see some facial features and variation. If you are going to put fanart, make sure it's your best and not the first thing they will see.