Ys I & II: I picked up the DS version because I thought "what the hell, it can't be that bad"... lol, holy hell it was worse. Two of my favorite games ever and I honestly couldn't be bothered to get past an hour, instead I just replayed the definitive TCD release for the umteenth time (on Virtual Console <3 <3).
Ys III: I originally played the balls hard SNES version, and ugh it was shit. Then I eventually played the excellent TCD conversion and all was forgiven. Why isn't this on Virtual Console yet?
Samurai Showdown: Loved this in the arcades, but when I played it on my SNES, ugh, all zoomed out visuals and muddy controls. Thankfully I was able to return it and pick up the (decent) Genesis conversion (who needs Earthquake anyway?).
Virtua Fighter: Got this with my Saturn, and found out it was an ugly 30fps piece of shit. Good thing Sega mailed me the glorious 60fps VF Remix a month later.
Silhoutte Mirage: I bought the PS1 version to support Working Designs. Shouldn't have bothered because it had like half the animation, no backgrounds and they fundamentally broke the game, so I just kept playing my superior Saturn import. Good thing SCEA cockblocked their Radiant Silvergun conversion, great games don't deserve this sort of treatment.
Grandia: Picked up the PS1 version and was treated to massive slowdown, nasty shimmering all over and possibly the worst localization I've ever had to suffer through thanks to SCEA (and on PS1, that's an achievement in itself). Even though it was totally in Japanese and I had to play with a FAQ in hand, it was totally worth dumping the shit PS1 port and playing the stunning Saturn original as an import. Thank god DC Grandia II came over and I could just immediately skip the somehow shittier PS2 conversion of that.
Super Monkey Ball Deluxe: Picked up the PS2 version for the extra puzzles, shouldn't have bothered because this game's practically unplayable on a Dualshock. Octo-gate 4 Lyfe!
Super Mario 64: Bought it on DS at launch, ended up just playing Feel the Magic instead. This game needs an analog stick, end of story. 3DSmake plz.
Street Fighter II Turbo: I made the mistake of buying this on XBLA. I'll never make the same mistake of buying an outsourced-to-western-shovelware-developer Capcom XBLA conversion again. It was literally unplayable, and that ass 360 D-pad wasn't helping either.
Sonic's Ultimate Genesis Collection: Bought this dirt cheap, loaded it up, was visually assaulted by the glitchy upscaling, and immediately went back to buying overpriced yet wholly superior Virtual Console games instead. In M2 we trust. <3