The 986 Boxster is a gem, but don't tell anyone how great it is. For those of us who know, this is one of the greatest Porsches to drive, own, and enjoy. It's truly a sports car you can drive everyday [I can confirm, I daily drove a 986 for several years!]. Right now the 986 is one of the best values in sports car ownership on the market today. Sure, there are a few things that can go wrong with them, but by this point most cars have either been upgraded or had these quibbles fixed. If you find the right one it could serve you very well for a very long time for not very much money. But, really, don't tell anyone how great it is, or it won't be a bargain anymore.
Here is a great story of a great owner doing the necessary fixes to a broken Boxster himself to get it back right again. In this case the cylinder head cracked, which can certainly happen, but isn't a common complaint among M96 engine owners. Instead of dropping the $13,000 that the local Porsche dealer wanted for the repair, this Porsche fanatic decided to undertake the process himself. By this point if you're interested in a twenty year old sports car, you either have lots of expendable cash, or you're reasonably mechanically inclined. Personally, I'd have no qualms undertaking a cylinder head swap myself, as these cars are really not that difficult to work on. Of course, it would be an engine-out procedure, but that's probably the most daunting part of it. If you take your time and make it work, it's reasonably easy to make a big repair.
Anyway, repairs aside, the early Boxsters are so delightful to drive that they're really worth any pain in the neck they might give you. I haven't experienced any pains of ownership with the M96 engine, but if I had, I'd still probably repair it and keep on trucking for another several years of ownership. If they're properly maintained and not overly stressed, these cars require little more than fuel, oil changes, and the occasional set of tires.
Don't take my word for it, listen to this owner tell his tale on the newest episode of Hello Road. (If you're not subscribed, I highly recommend it. Ethan is a master of the medium.)