Primer is a great movie. It is in fact "startup themed," although it is a little light on the business side of things; it's more focused on the product they design...
Micro Men from BBC had some startuppy themes when Acorn began, although it was more about the rivalry with Sinclair than the startup experience itself.
In my head I associate all kinds of survival movies like Cast Away, Rescue Dawn etc. being startuppy as well in the sense that the characters are surviving on their wits and persistence, against forces of nature and their own doubts.
I'm thinking of "Hyperion Bay" not completely about a startup though.
The series centered around Dennis Sweeney (Mark-Paul Gosselaar) who, after a successful career in the software business, returns home to open a local division for the company he works for. The series follows the drama when the new meets the old in the little coastal town of Hyperion Bay, California.
http://www.imdb.com/title/tt0390384/