In terms of 3D prince of persias, then I'd say The Sands of Time probably. It's the most consistent and well-paced.
People love praising Warrior Within but I played it again recently and it doesn't hold up. Lots of backtracking, lots of confusing camera angles and a frustrating world to get around. Dahaka is very cool though.
I don't remember Two Thrones enough to comment on it, but I thought it was pretty good at the time.
Prince of Persia 2008 is my 2nd favorite and it still sucks that they never followed up on it. There's a lot of room for improvement but it was a great entry.