"The Clone War" actually was finished before Balance of the Force. I got frustrated working on one scene in particular from Balance and made the bulk of CW (sans Dooku's yellow saber) over a weekend, as a change of pace.
I think that CW is still a tad rougher around the edges than Balance. If I ever had access to all of the extra Jar Jar scenes, the lost twenty scene, and the extra scenes from the Lars Homestead, I would definitely make a Special Edition to CW.
There are actually changes to nearly every shot in the Phantom Menace. I found that shaving a few frames off of almost every shot drastically reduced the film's final runtime. That's how I was able to add so much deleted footage and extend other scenes without really cutting out a large amount of footage in the finaly film, considering that it runs 16 minutes shorter and yet has all the deleted scenes and several new scene extensions.
There are a lot of really tedious changes I made just for the hell of it that I doubt most people ever notice. I'm thinking about making a website and putting up a comprehensive list of every major change (besides frame trimming).
A few changes that most people don't ever notice:
The first scene between TC-14 and the Viceroy has been extended with additional dialogue.
Original - Darth Sidious: I don't want this stunted slime in my sight again!
Balance - Dath Sidious: I don't want this slime in my sight again!
The Jedi mind trick now has its own sound effect.
When Qui-Gon and co enter Mos Espa, a large ship flew by at a very low altitude against line of sight. It had been digitally painted out of the shot in Balance. The wipe is trimmed to help hide it.
Beisdes the cantina song (if you've seen it, you know), Watto has several new lines of dialogue.
Original - Anakin: Since I was very little... Three, I think.
Balance - Anakin: Since I was three, I think.
Original - Anakin: Sandstorms are very... very dangerous. Come on, I'll take you to my place.
Balance - Anakin: Sandstorms are very dangerous. Come on, I'll take you to my place.
Dozens of "Phantom laserblasts" have been given sound effects, and lots of additional sound has been added in other places, such as additional chatter on the streets of Mos Espa.
Any scene where music has been replaced or aliens are dubbed has had the entire sound mix reproduced from scratch.
In the balcony scene with Maul, Sidious has an alternate line of dialogue. Digitally altered footage of Sidious had to be painted over the original scene and looped in such a way that it created the illusion of a lip synch. The footage of Maul had to be altered also to match the new length of the scene.
That's just a few of the lesser known ones...