I was in a similar boat a few months ago. I had purchased an 03S in all the options I wanted... PSM, 6 spd, right wheels, heated seats, bose, etc...
I took it in for service, and saw a brand new 06 (this is in 07) that the dealer hadn't sold. I figured I could swing a pretty nice deal for it since it was about to be 2 years old sitting on the lot in a few months time.
Regardless... I stll have my 03S, not because of price, but because of the car itself.
I had owned the 03S for about a month so had a good baseline.
Here's what my breakdown came to:
From the looks: (of course based on personal preference, these are just mine)
Body : 987 had an updated look on the exterior. However, I preferred the more aggressive look of my 986 with the rims and colored brakes and meaner looking and sounding exhaust.
+1 for the 986S
Lights :
My 986S had the halogens. The 987 had the lits...
+1 987
987 had a revamped interior which was significantly ROOMIER. However, I didn't like the "modernized" look of the controls etc so this was a tie.
Features:
My 986S is fully loaded with every option I wanted (except Xenons, but I'm installing HIDs on it this weekend). 987 was pretty stripped down.
+1 for 986S
Engine: Hands down, I thought the 986S was faster and throatier and had more lower end torque which really gave it an edge in the SeatOfThePants test.
+1 for 986S
Handling:
The 987 handled a LITTLE BIT better. It's wider, more stable... This was a tie, but I gave it a +1 for the 987
It was basically a tie for me. But then I had to ask myself. Why did I buy the 986 in the first place?
I had found a car that had every feature, every option, the right color combo, rims etc... I drove 400 miles to go get it!
So I stuck with my 986S.
You can't go wrong with either. It's a very close comparison and boils down to personal preference.
Go with your gut... or better yet, go with the 987S
There's no comparison there IMHO.
Thanks for reading this, hope it helped