Strange Days is fantastic. It worked particularly well at just that moment in time, with the LA riots fresh in mind and the millennium coming up. It's one of the best cyberpunk movies I know of, and horribly underrated.
It bombed at the box office, but critics generally praised it, and since its run, its critical standing has improved.
Frankly, I hated it. About 7 years later, gave it another shot, still hated it. I think it is the most depressing movie I've ever seen.
So it is not horribly underrated. By the critical reception and comments here, it is inscrutably overrated.
The others would be The Departed — I loved the original Hong Kong movie Infernal Affairs, but I couldn't bear to watch more than a few minutes of The Departed. And the David Lynch Dune.
Usually I tough it out, L.A. Confidential, for example, I thought was awful, but saw it through to the end. I couldn't believe that the same director (Curtis Hanson) could have made such an awful (though, stangely, lauded) film and also the absolutely amazing Wonder Boys (and the servicable The Hand That Rocks the Cradle).
But I choose to go by the former - far fewer people are aware of it or would list it as an important sci-fi/cyberpunk movie than it deserves.
I think my aversion to it is due to Ralph Fiennes' and Juliet Lewis' character portrayals. I would consider myself a fan of both, and I'm not saying they didn't act well. I am saying these characters should never have been created, as one is disturbingly nervous, the other disturbingly nasty.