Slightly used gen 1 S, or new gen 2 non-S?

[Brucelee]

ON a used S, you can get a lot of car for relatively little money. The first two years depreciation on a new S will kill you!

[Adam]

Even brand new 04 S's can be had in the upper 40k range. I know what I'd do.

[Pilot2519j]

I would opt for the S rather than the regular. Has more standard options: better brakes, more horses are the main reasons. Neither are dogs and both are quick and handle super great. I would favor it more for the brakes which are the 911 brakes stops you and a dime.

[Perfectlap]

If you are asking about buying a 986 S (3.2L) vs. 987 (2.7L)
I would say don't buy a 987 they have ugly headlights.

seriously, it would depend on how much you can get the 986S for.
If its not a serious mark down I would go for the newer car. I would look at
the likely depreciation of the two. My take is that you take less of a hit with a very popular used car. The pool of buyers is inevitably larger for people looking to spend 25-35K than those looking to spend 35-45K.
I got my 2000S for 30K with 10,000 miles last fall. Its my hope that it will be quiet some time before it get down to $20K. Historically I've never put more than 10K miles a year on my cars so hopefully that will help out over the next four years.

From a performance standpoint the power of the new Boxster is close to the old S model so you won't be making a huge swing either way in that department.
And I strongly feel that neither the S or the standard are underpowered.
Take both to a Porsche driving school and when you set the absolute quickets lap possible in either, then tell me you need more power. The Boxster is sportscar not a drag strip car, there is more than enough power to get you into trouble.
A friend of mine used to race junior formulas with a current f1 driver and he recently told me that this professional driver sent his father a new Mercedez compliments of the team. After driving it he STRONGLY noted that its 500+HP should not be sold to the general public. Even if you are only intending to drive in straight lines you need to master the power you have before you complain about not having enough ooomph.

[Onad]

You might also want to consider the type of driving you do. I went with the standard (non-S) for a lot of the reasons that have already been mentioned. I also drive far too much of the time in urban traffic so the base 5-speed made more sense to me than the six-speed due to the ratios. Some people disagree with this assessment, arguing the S is better for the greater torque at low rpms. Drive both and see what you think.

You can't go wrong either way, but I think you could save a lot of $ in both initial cost and depreciation if you went slightly used (S or non-S). Personally I never put much stock in the "only buy a S" argument. I think it all depends on your driving. The base car is slower below 3000RPM, but after that I think it's harder to tell the difference (several car magazines have also stated this, Road & Track, Excellence, etc.).

Since this ramble is all over the map, let me try to wrap this up. It's all about what you value:

1) If you value having the best available- buy a S model- otherwise you'll never be satisfied
2) If you value refinement more than anything else, buy the newer 987
3) If you want to limit your depreciation loss and initial investment, buy a used base or S (in my opinion, there are great deals on Certified 03 and 04 models right now-- with 2.9% financing too from PCNA). The Certified means your warranty will likely be the same or better than buying new.
4) The type of drving you do and whether or not the car will be a daily driver are other important factors.

Good Luck. You can't really go wrong.

03 Daily Driver