The 2000 contest is it for me. 1988 was great and had a lot of drama, but if we wanted to be picky, it also had two dunkers often overlapping and completing jams we'd all already seen from them in previous contests.
In 2000, we saw three tremendous competitors completing outstanding and unique dunks (and doing so on their first attempts! A lost concept!). And underrated, but even Ricky Davis (unknown at the time) brought something legit to the table (albeit too little too late): http://www.youtube.com/watch?v=QffErlP-MbQ
The contest in Oakland wasn't propped up by the fact that it was a star's hometown (unlike Chicago in '88) and it didn't have a pre-conceived rivalry (Wilkins vs. Jordan) so some would give the '88 contest an advantage in that regard. However, I'd also say that helps the '00 run. The dunkers created an incredible show from scratch. People expected something great from Carter and their expectations were still overwhelmed. And two other competitors would have walked away champions had they just picked a different year.