I would do:
Psychic: STAB, good power, high accuracy, chance to lower Sp. Def.
Ice Beam: Good power, high accuracy, chance to freeze, deals with Dragon types.
Shadow Ball: Mewtwo's signature move. Good power, high accuracy, decent chance to lower Sp. Def, used to deal with Ghost types.
Thunder: High power, good chance to paralyze.
Other good options are Aura Sphere, Taunt, Calm Mind, Light Screen, Reflect, and Selfdestruct.