Final Fantasy 1 - 3, 7 - 8. 1 - 3 have not aged well at all. 1 is nigh unplayable, 2 I have no idea how I was ever able to enjoy it, and 3...god damn..it pains me to think that this will actually be available in english on the DS at some point. For shame. 7 and 8 both featured pretty painfully bad storylines sprinkled with bad combat systems and characters that I loved watching die instead of ever developing any bond with.
Metroid - Another game that people remember fondly through nostolgia. Horribly unfun and buggy

Loved it as a kid, but there's no going back.
Legend of Zelda 2 - Jesus, how anyone ever saw this as a good game is beyond me. Shit graphics (even at the time), control, and dungeon design. A prime example of a big name pushing a shitty game's sales numbers up.
Snake's Revenge - this one is kind of cheating. A lot of people remember it as Metal Gear 2 and remember having a lot of fun with it, but holy hell was it a poorly slapped together piece of shit. The storyline was so bad it made Metal Gear Solid 2 look like Phillip K Dick and the side scrolling segements were painfully bad. Ugh.
Lunar - Oh god, don't get me started.
Vay - See Lunar and then multiply it a few times.
Shadowrun (SNES) - Let's see... let's mix a bad sci fi Sierra adventure game with Ultima 8 and see what we can come up with. The only reason people remember this game so fondly is because of the graphics (which look beautiful, and much like Ultima 8, they really do go a long way in hiding the shittiness of the underlying game from people just glancing at screenshots). Outside of the early Fed Ex Simulator and the lackluster graphics, the Genesis version trounced all over the grossly inferior SNES version.
Donkey Kong Country - OH SHIT, WE'RE SO CLEVER BECAUSE WE GO ABOVE 100% LOLOLOLOLOL. FIND TEH BANANAZ
Salamander - Sorry, I just don't memorizing games that much.
Rhapsody - Let's take a Strategy RPG, gear it towards preteen girls, and sell it to adult anime fanboys. Hillarity ensues.
Xenogears - They should have just called the game, "Clusterfuck".
Warcraft - They should have just called it, "Dune II with Orcs, Bridges, and Modem Play". Unoriginal as hell (par for the course when it comes to Blizzard) and overall just not a lot of fun. It was great to see Westwood steal a little of the interface from Starcraft for Generals and find a way to make it not suck.
Diablo - Click. Click. Click. Click. Click. Click. Click. Click. Click. Click.
Mortal Kombat - Maybe the series is to XXXXTREEEEEEME for me or something, I don't know.