Mine is Mario Kart 64 for one reason: the tighter control. I'm not at all a fan for the original Super Mario Kart's control, where I would always slide right out into the dirt whenever trying a power slide. Unfortunately, Mario Kart Super Circuit and Mario Kart Double Dash both seem to have the same control as Super Mario Kart, so I appear to be in the minority. As for courses, I prefer the layouts (much more importantly, the music) of the Super Mario Kart courses (heck, everything about the original except controls I like more than Mario Kart 64), but I can't enjoy them with the controls they have. And no, I'm not going to switch to a heavier character to decrease the difference.
And I was disappointed to see that Mario Kart 64's Rainbow Road changed the visual look (no more multi-colored blocks?) and music from the original. Rainbow Road from Super Mario Kart was my favorite Mario Kart music... but then, racing a Rainbow Road that had rails was nice.
Why I continue to try to save the world, I shall never know.