After-market alarms are known to cause this sort of problem. The stereo was mentioned and I've read elsewhere that stereo boosters(amps) can also be a problem.

Follow Arthur's advise and use an ammeter to find current draw. If pulling all of the factory fuses under the hood doesn't show a problem, you likely have trouble with something after-market.

For testing, read what Steve Brotherton and Arthur Dalton had to say in this post:

Normal current draw?