Dustin Hoffman has two roles, his revenge-seeking astrophysicist in Straw Dogs (which I haven't seen) and as Rain Man, an autistic savant. Shame on IMDB for confusing savants and mathematicians.
Russell Crowe gives an excellent portrayal of the hallucinating game theorist John Nash and Anthony Hopkins has a decent role as an older mathematician with dementia. But both these movies add to a stereotype connection between mathematicians and mental disease. Jake Gyllenhaal's math student in Proof (not nominated) better portrayed the excitement a mathematician feels.
Sean Penn gave a fine acting performance in 21 Grams, but the mathematics plays no role in the story or in how Penn portrays his character.
Jeff Goldblum in Jurassic Park plays the kind of scientist that always annoys me: lots of neat parables with no mathematical meat behind them.
I have heard nothing but contempt from my colleagues by the way Matt Damon's janitor turned mathematician is presented, and thus it wins the poll. At least Good Will Hunting does a nice job promoting the Fields Medal.
I did see Pi years ago but the movie was a confusing blur to me.
Which leaves my favorite, the TV crime-fighting mathematician Charlie Eppes portrayed by David Krumholtz. Reportedly Krumholtz hung out with Caltech mathematicians to prepare for the role and he gets it pretty close to right, a slightly shy, very smart and otherwise normal person who just has lots of fun talking and doing math.