I think part of the hysteria has to do with the fact that high performance sports cars have issues. And the advent of enthusist boards for sports car makes have allowed us all to see what issues affect a small percentage of all Owners. Below are a few examples I have experienced.
Previous to my 987, I owned a 2000 MR2 Spyder. After purchasing, I learned that the 1.8 liter Toyota engine had an issue with the precats crumbling, causing to much backpressure, and killing engines. It was supposed to kill all engines over 30,000 miles. I became concerned and pulled my manifold once and month, and eventually replaced with headers to sleep better at night. And then there was the oil starvation issue if the car was tracked, causing the engine to throw a bearing if I recall. All the MR2 guys were buying a $600 custom oil pan to save the day. That was when I decided to sell the car, since I was spending to much $$$ to solve issues that may not be entirely real.
Going over to the Elise board, same thing, the Elise guys were experiencing blown engines due to oil starvation, and either installing new oil pans, or retrofitting a scavenger pump and reservior system.
My memory is fuzzy on this one, but before i purschased by MR2 Spyder, I was also considering used S2000's. The boards stated that they we having gearbox issues that the dealer would not correct, warranty or not (and the 3 year, 36,000 mile Honda warranty does not last long).
And then there was the dread BMW M3 Engine failures on the early SMG equipped cars.
So, from all the information gleaned on this site from many more knowledgable people than myself, if you want a Boxster, purchase the newest one you can. The 05's seem to be a good value (2.7L) and will have a year of warranty on them.