It depends on what happened to yours when it went which will drive what needs to be replaced and the cost. You should definitely pull it apart to find out what you need (maybe a case....). Based on the cost you need to decide whether to rebuild or replace.
If you go with a rebuild your best choices are probably a Polaris crank kit (you get a lot for your dollar here) plus whatever else you need or Indy Dan.
Last year I completely rebuilt mine; polaris crank kit, crank case & pistons. Considering I had already replaced one cylinder and the stator I figured I had a brand new engine that would last me forever....until the exhaust valve broke this year. One cylinder, piston and 2 exhaust valves later I'm hoping it will last forever. However, I also have a 4 stroke which is absolutely amazing in terms of reliability and gas mileage so I'm currently looking to replace my 900.
My engine rebuild last year cost me around $2500 cdn for parts & shipping and I did all the work.