This is a great topic and there are some great answers here.
I would nominate Pink Floyd's The Final Cut. Not my favorite but not as bad as critics and fans made it out to be.
For Nirvana, I would think Bleach and Insecticide could be mentioned. Great raw energy and no one but the local fans dug it until Nevermind broke.
I poo poo'ed Metallica's black album when it came out. Master of Puppets it was not. But you know, it's not a bad album.
Geto Boys, the album with Mind is Playing Tricks On Me is hilariously bad and yet awesome at the same time. Bushwick Bill is an aquired taste to be sure.
The first Mr Bungle album. Jeez everyone I played that album for absolutely hated it. I think it's a masterpiece.
Yellow Submarine by the Beatles tends to get panned. The whole 2nd side is just George Martin's orchestral compositions. But it's good! And of course Hey Bulldog.
Marvin Gaye's Here My Dear. My goodness what a mess of an album. He only made it because he was contractually obligated to do so, with the stipulation that all proceeds went to... His recently divorced ex-wife. It is blunt. Clumsy. And beautiful.
I'll stop there. Not sure if I have veered away from the original intention of this thread or not. Looking forward to reading what others come up with.