I spent a handful of hours getting near-complete information on Bulletproof. The following moves are nullified when the target is a Pokemon with Bulletproof (same way that Soundproof does, doubles and triples interaction not tested):
Acid Spray (Acid Bomb in Japanese)
Aura Sphere (Wave Bomb in Japanese)
Barrage (Ball Throw in Japanese)
Bullet Seed (Seed Machine Gun in Japanese)
Egg Bomb
Electro Ball
Energy Ball
Focus Blast (Fighting Spirit Bullet in Japanese)
Gyro Ball
Ice Ball
Magnet Bomb
Mud Bomb
Octazooka
Seed Bomb
Shadow Ball
Sludge Bomb
Weather Ball
Thematically, every move had some sort of bullet-esque action or was named bomb/ball/bullet in either English or Japanese. I also tested all of the following moves, with none of them being blocked by Bulletproof:
Aqua Jet, Bubble Beam, Bullet Punch, Fire Blast, Flame Burst, Flash Cannon, Fling, Fury Attack, Hydro Cannon, Lava Plume, Moonblast, Mirror Shot, Mud Shot, Night Daze, Pin Missile, Self-Destruct (Explosion), Spit Up, Water Gun, Water Pulse.
If you would like me to test anything else, do let me know. Moves I cannot test right now but think might be plausible / worth testing in the future:
Aeroblast (Lugia exclusive)
Luster Purge (Latios exclusive)
Mist Ball (Latias exclusive)
Searing Shot (Victini exclusive, Flame Bomb in Japanese)
Seed Flare (Shaymin exclusive)
Techno Blast (Genesect exclusive)
Of these, Mist Ball and Searing Shot will be most likely the only ones that will be ignored by Bulletproof. The others are included mostly because they fit the flavor of the move pretty decently, and because why not.