I think the first one is the best of the bunch, too. There were certain aspects of the second one I really enjoyed, but overall, nothing compares to seeing the transformation of Peter Parker to Spider-Man. Probably the most well-done transformation of this kind ever - so well-done that you can almost believe it's real. They took the time to show him not just gaining the powers, but learning how to use them. So often, it's like "Oh, gee, I can fly" and then the character is flying around like Superman in the next scene.
Also, this third one didn't have as many great subtle comic moments as the first one. They tried - there was a line about "getting right back on the horse" (a little allusion to "Seabiscuit," perhaps?) and a couple of cute cameos for real Spidey/Sam Raimi aficionadoes, but nothing like the best line in the whole damn series:
Aunt May: You can't do everything. You're not Superman, you know.
(The best part of that was Tobey's/Peter's reaction. That's what Tobey's really good at - subtle non-verbal reactions. They didn't use his talent for that nearly enough in this one.)