The Republic comics are my favorite comic series in all of Star Wars so they get my vote. They work seamlessly with the PT, and they showed a bleaker version of the clone wars. Not to mention my favorite Rise of the Empire era master-padawan duo, Quinlan Vos and Aayla Secura is heavily developed here.

The Clone Wars (2008) for sure

Next is the Prequel Trilogy

I voted TCW but I'm also a big fan of the Dark Times comics.