My girlfriend has a 2007 Civic DX. The battery has been going dead mysteriously. I have checked the voltage with the engine running, getting 14+ volts, so the alternator is good. I did a parasitic battery draw test by connecting an ammeter between the negative terminal and the negative cable, and after it goes into 'sleep' mode, it's only drawing 0.005A, which should definitely not be killing the battery. I replaced the battery as well, and then tried a third battery in it, no change.
I'm stumped.... any ideas??

Probably unrelated, but the front speakers also stopped working recently. They came back on for a day or so, then went off again since then.

Note* Everything in the car is completely stock. No aftermarket audio or performance parts.

 

Try checking the wiring to that goes to the front speakers, it may lead you to what is causing the drain.

Things That Drain the Car Battery | eHow

 

I'm starting to think it isn't a drain at all, and that there is a problem with the starter. Drove it for two hours, shut it off, started it, it was fine. shut it off for 10 mins, tried to start it again, nothing. sounded like a dead battery. 5 minutes after that, started perfectly again.

 

At least on the old models, the most common failure of the starter was that it would get to where it sometimes click but not turn, though other times it would start normally. Eventually they would get worse until it never starts at all. I don't know if they still use the same type of starter on an '07.

You could rule out other stuff by measuring the voltage at the starter while someone turns the key trying to start (and it is in a mood to not start). If you have good voltage but the starter doesn't turn, replace it.