I have a soft spot for Quest 64 / Holy Magic Century on the N64. Story/characters & presentation couldn't be more bland but I always thought that especially the spirit/level up system was enjoyable and rather unique!
I also really love the SNES port of Doom. Frame rate and resolution-wise it's the pits but for me the awesome rendition of the classic MIDI music almost makes up for it.
Almost forgot Sword Of Vermilion. This one has a lot of troubles and is super uninspired as well, yet I somehow played through this several times.
I blame nostalgia...