Lets face it, there's a reason their cult classics; their the best, and their way underappreciated... apart from those that become successes through cult status (everyone seems to think adding Donnie Darko to their fb makes them appear profound).
Now the problem with that definition is clear; these are the very best the platforms have to offer, and no-one knows about them D:
So here's a few to get the ball rolling:
Tombi (think its called Tomba outside of UK), PSX:
This game got pretty good reviews, I honestly dont understand how it never took off. Maybe it was a little too 'kiddy', the whole idea behind it is a little ridiculous. For me its awesomeness is more nostalgia-based now but its still easily one of the best psx games out there IMO, and I wouldn't love it so much now if it wasn't so great back then.
Gotcha Force, GC:
The very definition of 'cult'. No-one I've met ever heard of it (except the guy that introduced me), yet everyone I introduce it to immediately falls in love with it, we even had a nice little community for multiplayer a few years back xD
This game received mediocre reviews apparently (I never witnessed them) and poor marketing (which I believe since I never witnessed that either), but even the developers cite it as one of their favourites.
Honestly this game far exceeds the limitations of the console, I'd go so far as to say it was one of the best games ever made, not just for GC.
So share you're hidden gems with us =]