When in doubt go with the "S". That said test drive both a 986 S and a 987 S. People tend to have rather strong feelings about which generation they prefer (due to size, performance, interior design, etc).
I personally like the looks for the 986 more. While the 987 has more ummph, it wouldn't be enough to have me dish out more money above a 986 S. The only 987 Boxster that makes me weak in the knees is the Spyder, but those aren't at their second round of depreciation yet.
Happy hunting.
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