Confide/Play Nice ignore Protect, lowering Attack or Special Attack.
Ghost's using Curse ignore Protect -the ultimate in saying "screw you" to Poison Healers stalling for HP.
Doom Desire and Future Sight ignore Protect. Future Sight is even vaguely widespread, though of course it's useless against Dark types and bad against Psychic and Steel types, making it problematic for using it to deal with Sableye.
Psych Up steals stat stages while ignoring Protect. Extensive set-up Pokemon trying to Protect-stall for healing while setting up can have the tables turned on them straight through Protect.
Perish Song ignores Protect, and Soundproof is in fact the only protection at all.
Interestingly, Role Play ignores Protect too. A bit niche.
And of course Phantom Force and Shadow Force bypass Protect. Yes, they're two-turn moves that fail against Normal types, but they can still cut the stall down -people will think twice about using Ingrain on the idea that with Leftovers they can Protect for 1/8th of their health a turn for free.
Sketch and Transform also ignore Protect, though this is fairly niche. (Hooray, I can Sketch their Protect?)
And of course the already covered Feint, Roar, Whirlwind, and Imprison all ignore Protect.
Also note that trying to stall for HP via Protect is a terrible idea in the face of a Dragon Dancer, Quiver Dancer, or for that matter a Pokemon that Shifts Gear, since they'll just stat-up until you come out of your shell and murder you, and then you'll have to PP-stall all their moves with Protect. Yipee.