I just got back on the site ... was looking at the "active topics" ... and I was first drawn to this thread because I can directly relate to it!
I've had my '06 D since March of '14. I've had to put a new battery in it every year since I have owned it! It's my first HD, so I thought that maybe that's just how they were ... Like the op Fred said, it gets pretty darn frustrating when you want to take the bike out and find that the battery is too weak to get the bike started.
I found the op's comment that the Power Commander (PC) was zapping his battery interesting ... because my bike has a PC III (might be a IV but I have to check?) on it too. Why would a PC drain the battery? I thought that it wasn't energized until the ignition was turned on? If I could, I wouldn't mind removing the PC entirely as it and it's pig-tail connectors take up a lot of room where there isn't any to spare.
Taxman mentioned the voltage regulator as a possible source of the power drain. I'm sure there has to be some way to test it? I know my alternator is good as I recently tested it after reinstalling the stator following the cam-drive triple-sprocket bolt replacement (yeah, mine fell out apparently like a lot of other rider's triple-sprocket bolts).