For the 987, I'd suggest not going for the first year it was in production. Typically, they work out problems from the first year and improve it throughout the years. There is some info on the 987 here (more info on this forum geared towards the 986):
http://986forum.com/forums/general-discussions/29258-2005-porsche-boxster-purchase-owner-issues-print.html. With what ever one you decide to purchase, I'd recommend a PPI to make sure you know what may or may not be a problem area with it. Hopefully some others will pop in with some additional advice as well. We do have some tech articles with information here:
Porsche Boxster 986/987 (1997-2004) Technical Articles | Pelican Parts to read up on. Good luck!