Can you feel this gooseBUMP?
Why the fuck no one mentioned Teenage Mutant Ninja Turtles IV: Turtles in Time yet? It is the best Beat 'em Up ever made. You had a bunch of cool ways to beat the crap out of the foot clan, from sliding, tackling, slamming them on the floor to the legendary screen throw. If you played this as a kid you went totally psycho the first time you saw the screen throw. It is madly fun, has beautiful visuals, cool music and a fair level of dificulty with the exception of Slash, the prehistoric turtle, hard as shit. The fact it is ranked ABOVE excellent games such as Streets of Rage 2, Final Fight, Cadillacs and Dinosaurs, Golden Axe 3 and Knights of the Round voices just how good this game is. And it is Ninja Turtles. What kid of the 90s didn't love the Ninja Turtles?
How the hell Portal 2 only got one mention? I do not think I need to explain how good Portal is and yet the sequel managed to be better if only for being righteously long. Also a denser plot and a potato. Go play Portal 2.
Perfect Dark is one of the best FPS ever. It was THE shooter of its generation. I vividly remember the first time I played it, I felt so thrilled I can hardly put it in words. And this is from someone who had played GondenEye nonstop for years. Perfect Dark has amazing visuals, sound, gameplay, okay story and a fantastic single player mode and much more complex mission objectives than seen before. The enemies had incredible and very organic reactions and blew everyone's mind at the time (he's begging for his life and suddenly pulls a pistol at your face). It also featured a Training room in which you learn how to use gadgets, are taught basic combat skills, unlock classic GondenEye weapons in the shooting range and get to know the main characters' profiles and the background of the game, while a soothing, relaxing music plays.
And you know what? Screw all that. The best part of the game was the multiplayer mode and you know it. Be it with 3 friends, up to 8 CPU-controlled bots, each being set with a different difficulty and personality/trait, or all together, the fun is guaranteed. The Challenges you need to beat to unlock all that range from retarded to retardedly difficult. Ever tried to hack a computer while a maniac chased you with a Rocket Launcher? Between a miriad of maps, scenarios and weapons, few things made a kid happier back in the day than a N64, 4 controllers and Perfect Dark. Mayhap all that plus Smash Bros. The one flaw I could point out in the game is the necessity of an expansion pack.
Already mentioned are Shadow of the Colossus and Chrono Trigger. I wanted to mention Super Mario 64 but seeing as many people here consider Super Mario Galaxy 1/2 overall superior titles, I will wait until I play them. In my heart, I find it difficult though for a game to ever top Super Mario 64, to me it is the pinnacle of 3D platforming like Super Mario Bros. 3 is the pinnacle of 2D platforming.
My favorite Sonic game is by far and wide Sonic 2 but I never beat Sonic 3 & Knuckles and am yet to play Sonic CD so I will hold that.
Street Fighter 3: Third Strike - Fight for the Future is regarded as the best fighting game along with Guilty Gear Accent Core. Both are very, very enjoyable and extremely deep and the only big flaw are the learning curves. They are also quite niche.
Honorable mentions go to Super Mario World, Super Mario Bros. 3, Portal, Street Fighter II' - Champion Edition and Chrono Cross.
Extra honorable mention goes to GoldenEye. The first time a FPS ever felt right on a console was in 1997, Nintendo 64. Precise controls, true mission objectives that required some planning (blow shit up doesn't count, sorry, Doom), addicting multiplayer, it had everything. Halo, Call of Duty and all others owe in part what they are to this game.