I saw the prequels as I was growing up. It's funny how I had glowing opinions of them then and now as an adult my opinion is completely different. It just goes to show who George's intended audience was.
But still, I like a few things. I guess I really more like the ideas of things, not necessarily how they were executed (looking through the responses already I think some others have made similar statements).
With today's movie technology, stuff like Avatar has proven you can do things in all CG and it can look really good. But the prequel movies tried that too soon, and watching them in high-def everything looks entirely artificial. Great artwork and designs, but just would have been better if he had used them more practically and CG more sparingly. (I guess it could be argued that if George hadn't pushed it too much when he did, the technology wouldn't be as far as it is now? I don't know.)
Anyways, things I like most:
TPM:
Liam Neeson, doing his best with the awful script. His rouge-ish sort of nature is a welcome sight among all the other stiff Jedi.
Parts of the podrace, minus the silly bits. (Side note: Hal's edit of it works really well)
The final duel, particularly the final part between Obi and Maul after the barrier comes down. Ewan McGregor does a good job of showing Obi's emotion through his fighting.
Palpatine causing the whole thing to happen just so he can become Chancellor.
AOC:
Coruscant, especially the Blade Runner type vibes from the night setting and the underworld parts.
Count Dooku, or at least the premise of his character, he was woefully underutilized (particularly in ROS). Christopher Lee was excellent.
The CG yoda looks so much better than that terrible puppet in TPM.
The brawl between Obi and Jango was cool.
The sound (or lack of) with Jango's depth charges was also very cool.
ROS:
The glimpses of the huge space battle at the beginning was really visually impressive. (wish we saw more of that)
Palpatine pulling all the strings behind-the-scenes was a really neat idea (its too bad McDiarmid didn't have a better script and a better actor than Christensen to work off of)
The Order 66 montage, the music was very effective and its very moving (despite that blue Twi-Lek's death being super dumb looking)
Yoda decapitating those two troopers on Kashyyyk.
Obi at the end "You were my brother" Ewan brought some good emotion to that scene.
The ending scenes remind you of the Star Wars movies you really like, which is nice.