Oil Pump Nut
The S52 is an exceptionally stout, reliable, and bullet-proof motor. There are very few internal weaknesses. That said, the Germans haven't figured out how to make anything out of rubber or plastic, so all of your accessory belts, pullies, gaskets, etc should be replaced now while it's cheap and easy- as already mentioned.
The S52 has only one design flaw that can result in catastrophic engine failure (other than the shitty cooling system)- the Oil Pump Nut. Go over to M3forum.net and do a search for Oil pump nut to learn more. Definitely address this while the engine is out of the car.
SOLD- Now Enjoying Honda Civic