Advice needed

[Mark_T]

All things being equal, I'd go with the manual, strictly from personal preference. The color scheme would be a part of he decision for me too.

[Spinnaker]

You have to answer a bunch of questions for yourself.
Is this a car for fun or a daily driver.
If you drive in stop and go traffic each day, you will get awfully tired of the manual. If you drive it for fun, there is nothing like rowing it through the gears in some twisty roads, especially the ones that go from San Jose over to the coast.
What kind of driver are you? Some are satisfied with the power of the regular Boxster, or want the power and torque increase of the S? Do you want to flirt with the CHP on occasion, or drive within the legal limit. If you get up to San Francisco a lot, you will hate the manual on the hills and burn up the clutch a lot faster too. Seattle has a lot of hills, so I know this by experience.
Do you like to work on cars and get your hands dirty? Any Boxster as old as these will need work of some sort, unless the previous owners were very deligent about maintenance. Repairs cost a lot so unless you have a fat wallet, beware. Get a PPI before taking the plunge.
Read the "Introduction to the Boxster" section of the forum to get an idea of what the ownership of this car will do to your life and wallet.
Buying a Boxster will change your life in many ways, some of them you have no way of knowing until you experience it. If you do take the plunge, you will see what I mean and I am not talking about the expense or money.
Would I do it again if I knew what I know now? In a heart beat.

[DenverSteve]

As you state - all things being equal - the newer, lower mileage vehicle. I've owned both and you'll notice little difference between the S Tip and Base manual. All things being equal you will love either.