Hardtop - very few of the newest 987 model designation cars (from 54 plate onwwards) came with them, so findign a car with one or a used one on ebay isn't easy. If you want the hard top for security reasons and you intend to use it all year round then its worthwhile. If you only want it for the winter then its one heck of a lump to store, even when hanging against a garage wall.
Sat Nav - everyone has an opinion but even the latest version doesnt allow full post code search. The screen is a bit low in the dashboard for my liking, you can't add speed camera locations and a map update costs £400 a time from Porsche only. In no circumstance pay extra for a car with it fitted IMO
RMS - rear main seal oil leaks - Porsche tend to honour these under goodwill or warranty nowadays, earlier cars are more affected and its not huge numbers, cars after Sept 05 have the latest seal which seems to be pretty effective.
Intermediate shaft Failure - not a massive problem, but when it goes its a new engine, which is £6k from Porsche with 50% goodwill if you have no warranty. 2006 cars have a revised bearing design, but its still not 100%. If you search the forums it'll frighten you to death - but bear in mind there are over 100,000 Boxsters built since 1996.
Warranty - Porsche now wnat an annual inspection completed and any issues rectifed before they will issue a new warranty. Warranty is now £1150 per year. You must have all servicing any repairs completed within the Porsche network to stay within the warranty. Tesco will give you their 'Finest' warranty for £420pa and you can have service and repairs outside the Porsche network at 40% cheaper costs. I don't know of anyone claiming a full engine on the Tesco warranty scheme yet.
2.7 or 3.2S ? - not that much different in running costs (3-4mpg worse on 3.2). 2.7 is a decent enough engine with 245bhp, but the 5 speed box can make it feel more sluggish than the torquier 280bhp and 6 speed S.
]); I have full leather sports seats and never found, even on a freezing cold day, the leather seats freezing cold; maybe it is the leather care I use (?) but even before I started feeding the leather, it has never been the case that I felt the car needed the heated seat and it would have made mine and my passenger's cold spring drive more comfortable but when driving on a sunny Winter day or Spring day without the Wind Deflector it has been a case of pulling aside putting the deflector on or put the hood up. 
