I can't pick one!
The first movie had the best story because it followed the book pretty closely with only a few deviations. This was the early 90s though and CGI was rather limited. For it's time, it was quite a breakthrough, never before had they used computer input puppets to get the rough animation for all the dinos.
The second had the best acting, although this may just be my bias because of how much i <3 Goldblum
Other than that, The Lost World also had a lot more action than the other 2. However we didn't see a whole lot of different dinos, nothing wrong with that though.
Jurassic Park III had the worst story and action, but the best dinos. I don't think raptors ever looked cooler than how they did in JPIII. Not to mention with CGI, they were able to play off the pack hunting mentality a lot more.
All in all, I like all three movies, but if i had to pick just one... I couldn't. How about some cool pictures of the JPIII raptors? :D
Sorry, I'm a huge rpator fanboy!