With a new '09 you obviously have the benefit of a warranty during your entire projected 3 years of ownership. That said, your greatest expense will likely be tires. Depending on how you drive and the type of tires you choose, figure fronts will last 15k and rears 10k, roughly $800/
pr installed, assuming they're 19s. Beyond that you'll have oil changes at $100-$150 a pop every 5k miles.
Tires and oil changes should be quite similar on an '06/'07 C2S. You didn't mention the mileage of the car(s) you're considering or how many miles you plan to drive per year. Assuming you'll have little to no warranty left, there's certainly potential expense there. If you plan to drive 5k/yr you'll likely be in for much lower r&m than if you're driving 15k/yr over 3 yrs.
My '02S is now at 72k and is my daily driver (~12k/yr). Over the long term I anticipate $2,000/yr in r&m, including $800 for tires, but I'm able to do a fair amount of basic maintenance myself to keep costs down. Without sweat equity I'd assume $2,500-$3,000/yr.
It seems to me that if you can afford to buy a ~$60k C2S, $1-$2k per year in maintenance cost over buying a new '09 Boxster shouldn't be an issue. Depreciation is going to be a far larger cost for either car. This isn't a dollar and cents issue. Go with the one that gives you the most enjoyment.