Almost anything could be wrong - something could be keeping the computer awake (it should go into standby mode when everything is off), or you could have something as simple as a under hood light, trunk light, or glove box light stuck on.
After confirming a good battery and alternator, I would follow the advice earlier in this thread of using an ammeter to check the parasitic load with the key off and all doors closed.
One tip I'd like to add for that is that you need to keep the ammeter hooked up for a few minutes with everything off and all doors closed and everything off. Load will probably be high at first because everything will wake up when power is reconnected. A shop manual will help with this process since it should list what an acceptable load would be, and if you need to do anything special to test it (on some cars, for example, the hood switch for the security system may have to be closed or disconnected for the computers to go into standby mode). It should also list how long it takes for the computers to go into standby. Also, opening any doors or any other disturbances may wake one or more computer and you'll have to start all over with your tests.
Electrical diagrams will also help with this process if you have them, assuming you find a fault in the system with the parasitic load test.