Have others had a problem with batteries dying in 2006 Legacys? We purchased a 2006 in that fall and are just now on its fourth battery. Batteries keep dying. Garage suggests we’re letting the car sit too long without driving it. 5 days!??
I would put money on it that there is something in the car that is constantly taking a draw off the battery. 5 days is nowhere nearly enough time to drain a battery without having something to drain it. I work at a subaru dealership and we let cars sit on the lot for much more than 5 days without starting them and we never have a problem unless something is taking a constant draw off it. Check to make sure the glove box light switch is working properly. Ive heard a lot about those and have replaced a few of them. Also the light under the hood. Sometimes these switches to shut those lights off dont always work. Do you have any aftermarket equipment installed on the car that is electrical? (Example: CD player bought somewhere besides subaru?) This kind of equipment can void your warranty if something electrical like that goes wrong. Check little things like that and if nothing comes up, bring it to your local subaru dealer and have them take a look. It should be covered under warranty if its isnt something that has been messed with by aftermarket equipment.
You should be able to let the car sit for at least a few weeks and be able to start it up without any aid. If the batteries are being damaged some how then the alternator is suspect. The charging voltage to the battery while the engine is running at around 2,500 RPM should be between 13.5 and 14.8 volts DC. The voltage should also be checked for any AC getting to the battery. There should be less than .1 volts AC. If the voltages aren’t within these areas then the alternator, or the wiring to it needs to be worked on.
There may be a current drain problem on the battery as the previous poster suggested and you need to see if the current drain on the battery exceeds more than 80 milliamps while the car is parked.
I just bought an 06 Legacy 2.5i in february, and i have just recently noticed an increase in noise coming from the alternator. This is probably due to the sound system I have put in the car. I notice when I turn the ignition switch just to have the battery on, I hear this consistent whining noise. When I turn the car on, the alternator begins to whine. This may be linked to a bad battery? This is such a coincidence because I recently recieved a coupon for testing/charging my battery at my local Subaru dearlership! 
I have not noticed any issues with the lighting/slow ignition/decreased performance of the sound system yet. I am definetly buying a voltmeter tomorrow to check the voltage.
Thanks for the advice about the light switches and will pass it on to the service manager (anonymously). I’ve had the car in to the dealership every time the battery has died (have lost track of how many times with each battery). The second battery had a dead cell (discovered when I had the car towed in rather than jump started). The third battery was installed last October–no problem until mid-April when it went dead and was replaced. The garage swears they’ve tested everything they can think of, including re-setting the motion alarm to “less sensitive”. (We never set this to begin with.) No aftermarket equipment. I keep hearing the comment that we just don’t drive the car enough. NEVER had this issue with our previous Subarus ('89 and '92). I have trouble believing that I’m supposed to remove some fuse when I plan to let it sit for a week or longer. 
Thanks to you, as well. I don’t remember the garage saying anything about the alternator but will bring it up. They have assured me that the “parasitic draw” is “normal.”
This is a total misdiagnosis. It’s always possible to get a new car with a bad battery but not four of them. No way on earth; unless you’re the unluckiest person ever born.
This sounds like an abnormal parasitic draw to me no matter what they say.
If you want to do a quick test (and assuming no VOM, test light, etc) make sure the battery is fully charged with the battery negative cable disconnected. Lightly touch a sharp edge of the neg. cable end to the battery negative post in a subdued light (dusk, in a garage, etc.).
If you see a bright blue spark, even a small one, then you have a parasitic draw worth worrying about. If you see a faint yellow spark then this could be ignored since that is probably the clock at work.
That’s not a real scientific testing method but can work in a pinch.
(And a good battery is not going to go flat in 5 day on its own.)