Cutthroat Island. Geena Davis hamming it up as a pirate - what could possibly ever be bad about that? Yet critics and the paying public hated it with a passion.
Robin Hood: Prince of Thieves (the Costner one). Costner can't do an English accent to save his life, and the critics pilloried him (and by extension the whole movie) for it, but get past that and this thing's great!
The Golden Compass. Bombed in the US largely because of - well, let's just say politics - which is a crying shame, as it's really good.
SW Ep I - The Phantom Menace. Yes it's bad, even though it made craptons of money, but I have a soft spot for it - and lines from it are constantly floating around our games...
"Wipe them out. All of them." - common instructions to summoned monsters; also often said by villains
"Why do I think we've picked up another pathetic lifeform?" - the party acquires an NPC or rescues someone
"There's always a bigger fish." - when you find out there's a bigger BBEG behind the original BBEG
"[We're] losing droids, fast!" - when party members and-or allies are dropping like flies