I like both the 986 and 987. And while the 987 is probably the better car, the 986 is truer to the Boxsters inspiration the 550 Spyder. Every update like the larger vents on the 987 is a departure from that original concept.
If I had to guess, in 20 more years the '03-'04 986 will be the most collectable, followed by the other 986's. And with engine failures affecting the majority of Boxster's (like 99%), the surviving few will be worth a fortune by then.