Here are all the ones I could find:
Shaymin Sky form learns:
- Quick Attack (instead of Synthesis)
- Air Slash (instead of Aromatherapy)
- Leaf Storm (instead of Healing Wish)
- Air Cutter, Ominous Wind & Tailwind (instead of Earth Power & Endeavor) by move tutor
Rotom learns a special move when it changes form:
- Mow form: Leaf Storm
- Fan form: Air Slash
- Wash form: Hydro Pump
- Heat form: Overheat
- Frost form: Blizzard
Wormadam learns a few different moves by level up, move tutor and different TMs. Below are the level up differences, go to the Wormadam pokedex to see all the other differences because there are a lot.
- Plant cloak: Razor Leaf, Growth & Leaf Storm
- Sandy cloak: Rock Blast, Harden & Fissure
- Trash cloak: Mirror Shot, Metal Sound & Iron Head
Deoxys learns some different level up moves:
- Normal: Knock Off, Snatch, Recover
- Attack: Taunt, Superpower, Zap Cannon
- Defense: Spikes, Counter, Mirror Coat
- Speed: Double Team, Swift, Agility, Extremespeed
Giratina and Arceus have the same moves regardless of form.