From a director's point of view Peeping Tom and Heaven's Gate are the obvious ones. It's really rather sad that arguably Britain's greatest film director saw his career ruined because of a film that's now regarded as a classic.
No mention so far for Ryan's Daughter. Didn't quite destroy David Lean as he then went on to make A Passage To India but the critics incinerated it. There was a rumour than Stanley Kubrick committed suicide because of the negative feedback for Eyes Wide Shut.