My turn.
In TPM I liked:
-Watto
-Liam Neeson's performance, but not so much his dialogue
-The podrace, except for the announcer and some bits with Anakin
-The three underwater monsters in the "Core"
-Theed
-When the doors in the Naboo hangar open to reveal Darth Maul (I think that should have been the first time we see him though)
-Most of the Obi-Wan & Qui-Gon vs. Maul battle
-The MTTs and the AATs
-The way the battle droids came out of the MTTs
In AOTC I liked:
-The arena battle on Geonosis
-Most of what had to do with Obi-Wan, especially...
-Everything with Jango (excluding Boba's part in it)
-Dooku
In ROTS I liked:
-The emotion in it, it didn't seem so fake and unemotional like the other two
-Most of the Anakin vs. Obi-Wan battle
-Order 66: the emotion and the different planets especially, but not the Anakin bit
-The reason Anakin turned to the Dark Side (the way it was done was pretty bad and too sudden)
-Utupau and the whole battle, including Grievous
-General Grievous and his wheel bike
-The opening scene up until the buzz droids came along, but they weren't that bad
-The scene with Anakin and Padme before Anakin decided to go help Palpitine
-I also like Yoda's confrontation of Sidious, but it could have been better
Overall I liked:
-The way Palpatine/Sidious was manipulating everything, and Ian's performance overall (though it was overplayed for his transformation scene)
-Mace Windu and his purple lightsabre (I would have liked it if there were more purple lightsabres and some yellow and orange ones too, to spice things up a bit)
-The gradual change of the spaceships towards the OT designs
-The Naboo starfighters and ships
-The Jedi Temple and the look of Coruscant
-The score, especially Duel of the Fates, the stuff that played during Order 66, and the emotional music during the Anakin Padme scene with Anakin alone in the council chamber