There is too many to name, so I narrowed it down to 5 games:
Fire Emblem: Radiant Dawn (Wii) - People complained about it's gimped support system, non upgraded graphics from the GC prequel, it's massive characters selection that many found pointless, and it's difficulty. I say forget all that, the graphics are smoother and animations look better, the difficulty is welcomed (I hate easy games), and the characters that join you add to the story since so many people from other Nations are being affected by the threat of the world and want to bare arms to change it and fight. Replayable Value is epic (finished the game 3 times and each run taking at least 75+hours) because they are many unlockable characters and events you can't trigger on your first playthrough. Plus, the story and it's music is the best of the Fire Emblem series IMO.
Legend of Zelda: Phantom Hourglass (NDS) - Yeah many fans didn't like the controls and at times they weren't responsive. Also, there were times you had to draw out a shape to open doors and it wouldn't be responsive as well. Still, this is one of the funniest Zelda's of all time and also has the most memorable cast too. Also the items you acquire, the final boss fight, the epic twist in the final boss fight, and the ending really rank high amongst the series for me. Finished it 3 times.
Super Metroid (SNES) - Didn't sell well, and many people didn't like that one has to explore without anything or anybody holding your hand. F that, this is one hell of a game and one of the best games of all time. The Soundtrack, the atmosphere, the protagonist, the villains and the Ending just define what classic is to me. One of the first games I've speed ran (best time is 4h 32mins when I was 11 years old). The Mother (pun intended) of all modern platformers that spawn many other classics (Castlevania:SOTN anyone?) and of Speed running as well. Finished it 4 times.
Street Fighter Alpha 3 (Dreamcast) - Many say this game is just a gimped version of SFA2 and that the soundtrack was better for it too. Those people must have played about 5 mins into the game and never picked it up ever again. Man this game defines my teenage gaming years. This is the most complete technical fighter of all time with loads of fighting options and great character balance. The story and the text scenes for each fighter were epic and added a lot of detail to each of them. The soundtrack and the stages are also memorable, for each song and stage really defines the character you pick. Since then, character development and story for fighting games have gone the way of the Dodo. FInished it countless time, at least once with every character.
Pokémon HeartGold/SoulSilver (NDS) - Actually people don't really bad mouth the remake of this game, probably since the OG was the best Pokémon game of all time. That's until this one came out. The added content to this already massive game will add about 20-40 hours to your play time, and since the OG was so ahead of it's time they didn't need to revamp it too much. The improvement of graphics, animations, addictional and remixed music, and expansion of the pokédex to 493 pokémon at the time just made this game even more perfect than it was 10 years ago, a feat once though was impossible.
Notable games: Fire Emblem: Awakening (I wanted so badly to talk about it but wanted to cover only one game per series), Legend of Zelda: Ocarina of Time (too perfect for this thread 
), Resident Evil: GC Remake, Pokémon Gold/Silver/Crystal OG, Street Fighter IV, Metroid II: Return of Samus, Super Mario RPG: Legend of the Seven Stars, Resident Evil 4, Phantasy Star Online, World of Warcraft, Starcraft, Warcraft III.
