Do you say twenty eleven or two thousand eleven?

Depends on what you are referring to. Either would be acceptable in the right context. However if you want the actual proper way to say the year it would be TwoThousandeleven. In normal passing, informal speech would warrant twentyeleven.

I say two thousand eleven, but everyone has their own preference for pronouncing years.

No, say two thousand eleven.

Twenty eleven I would say.

two thousand and eleven.

two thousand and 11