1. Obvious: The shot on Tatooine of Owen looking out at the suns.
2. Grevious re-entering his ship to get to the escape pod. This one is a bit more obscure, and maybe it was just me, but that hatch looked virtually identical to the one that Lando used in the end of ESB.
3. Leia's Theme during the short time on Alderaan.
4. (Invoking TPM) Duel of the Fates during the Mustafar duel.
5. R2 started hooking into computers again.
I saw more, I know I did, but I cannot seem to think of them right now.