Ok, first off I'm leaving off FPS's since they really aren't my thing anyway and I'm much much much more willing to vote against them just because. Also I should note, my favorite games are JRPG's so I'm much more likely to be biased towards them.
Space Invaders - Galaxian all the way! Asteroids, now there is a game I love, I could play that all day.
Metroid - Own it, hate it. Maybe it's from being so young when first gotten, but I never liked it and it's the only Metroid game I've played or ever will.
Zelda II - I don't like the gameplay. I fail to list the original here because I never played it until many years after playing both Link to the Past and Ocarina of Time (both of which I love).
Teenage Mutant Ninja Turtles II - Either in the arcade or the NES this is the one I most remember people loving. This is also the one I like the least of the first 4 TMNT games (I like it just fine but it fails to "blow me away").
Earthbound - It's ok at best.
Mortal Kombat II - To be fair, I suck at fighting games. I never managed to get to the last guy on "very easy" difficulty.
Street Fighter II - At least I managed to beat this one! With Ryu...spamming hadoken.
Secret of Mana
Super Punch-Out - The original is amazing, this one is ridiculous.
Final Fantasy V - The job system is fantastic...I just can't get into it.
Mario Kart 64 - Am I the only one who doesn't like this game but likes all the others? I don't even know why, maybe there are memories involved that I've blocked out.
Myst - Again, maybe from being too young (or stupid).
Madden - any, ever.
The Elder Scrolls series
World of Warcraft
Ico - I couldn't stand playing more than 2 hours of this. I was just far far too bored. And I wanted to throw that girl off a ledge and be done with it.
The God of War series - Meh.
Guitar Hero (or any similar game) - The intrigue of fiddling with that guitar to play a song I'd either rather not listen to or would just enjoy is zero.
Metal Gear Solid 2 - For a game that's supposed to be a lot of sneaking around I felt like I was in an action game most of the time. I didn't get too far.
Final Fantasy: Crystal Chronicles - I never hated a moogle so much.