You mean besides the account of the Clone Wars that was kept as an S-Canon rumor due to the fact that anyone witnessing the actual attack by clone troopers on the Jedi, without knowing of Order 66 would see them as insane? That was pretty much it. The actual storyline in The Thrawn Trilogy is still considered C-Canon.
1. The entire cloning technique. ie the force affects clones and so fourth
2. cloning jedi -not cannon does not happen
3. Luuke skywalker
4. no sith after vader and the emperor are killed (so no master C'boath )
5. The entire Nogrhi story doesn't happen. (we know where Anakin is during the clone wars)
6. The Katana fleet doesn't exist.
7. The idea that there was a Sith lord guarding the Mountain on Wayland.
and those are just off the top of my head. If I actually sat down and thought about I could find many more.