1. Zelda: OoT
2. SM64
3. Age of Mythology
4. Mario Kart 64
5. MGS2/3 tie

Honorable mentions:

SMB3
SSBM
SSB
MGS1
Zelda: MM
Zelda: TP
GoW II

1....SUPER METROID! HELLO PEOPLE! GO OUT THERE AND PLAY SOME GAMES!

2 thru 5...they dont matter

im sure prime one will be in there somewhere, tho :)

1.) Zelda (Ocarina of time)
2.) Super Metroid
3.) Halo
4.) Super Mario Bros. 3
5.) Mortal Kombat II (Arcade)

Top 3 games are easy, the next two really depend on my mood.

1) Final Fantasy VI
2) Tetris
3) Chrono Trigger
4) King's Quest VI (go go Zack & Wiki)
5) Super Mario Bros 3

Puzzle- game Tetris on gameboy with the sound off (runner up Bubble Bobble)
Strategy- Civilization II Gold (runner up Age of Empire 2)
Fighter- Bushido Blade (runner up 2D Fighting Super Street Fighter II Turbo)
Casual- Wii Sports (runner up NES pack-in Super Mario Bros/ Duck Hunt/ World Class Track Meet)
RPG- Chrono Trigger (runner up FF6)

However, within a couple months Bushido Blade may be replaced with Brawl and Wii Sports may be replaced with Galaxy.  Square could also release another fighting game on the Wii so you never know.  A new version of Civilization is coming out, so you never know.  There is even a chance that FF6 will beat Chrono Trigger if the rumored voice acting version ever comes out on the DS. 

 1. Ocarina of Time

 2. Twilight Princess

 3. A Link to the Past

 4. The Legend of Zelda

 5. Wind Waker

1. Legend of Zelda: A Link to the Past (to me it's perfect in every way. It's was 2D games should be like and it really made zelda what it is today)

2. Mega Man 2 (Another game that I think is near perfect. It's what platformers should be like. No matter how many times I beat this game I always come back for more. Mega Man 1 got this franchise's foot in the door and Mega Man 2 blow the ******* doors off the hinges.)

3. Mike Tyson's Super Punch-out!!! ( I absolutely love this game and is one of the best boxing games ever. It's formula was great: funny and crazy characters, awesome gameplay, and a hard boss battle. It's just too bad this franchise ended in the SNES era, although I couldn't see it out of 2D so maybe it was for the best....A new Wiiware 2D Punch-out would be awesome, but that's wishful thinking at best...)

4. Goldeneye 64 (Another great game. This game did many new and great things for it's time. For one it created a great multiplayer FPS experience that hadn't been done before. Secondly, it showed that movie games can be good, which wasn't the case before this game(and it's rarely the case now). I know my brothers, my friends, and I put many many hours into this game, and loved it.)

5. Super Mario Bros. 3 (Another great game here. This game took everything you knew about Super Mario and made it better. It added many new cool things like the use of suits and the selection of levels. The graphics for it's time were very nice as well. To me it is the true sequel to Super Mario Bros. because the US SMB2 was good, but come on it was doki doki panic and the Japanese SMB2 feels more like extended levels than a sequel.)

Honorable Mention:

Zombies ate my neighbor: ( I really like this game. It was one of the first games that I played it had great co-op play. The levels are funny and fun, and the same time they are challenging and require teamwork and communication with 2 players.)

Rygar: (This game was quite fun. it had lots of action and fun environments and very challenging because it had no save option so you have to beat it in one sitting. Also the music was awesome and I still can hear it in my head.)

Gun.smoke: (Another cool NES game. It's my favorite western game and that's saying a lot cause I don't really like western games. It had fun, simply gameplay and fun bosses and levels.)

and many many more....

PC pick:
Diablo II: ( this game is my favorite PC game ever. It was just so great. The gameplay, levels, enemies, bosses, powers, and weapons were all awesome. The online play was like no other and best of all free. I spent way too many hours playing that game into the wee hours of the night.)

Yeah I'm kind of an old school gamer. I probably sound like an old man, but rest a sure I'm only 19...

1. Donkey Kong Country
2. Super Mario 64
3. The Legend of Zelda: A Link to the Past
4. Tales of Symphonia
5. Baten Kaitos: The Eternal Wings and the Lost Ocean

I only put in one game per series, otherwise it'd have been impossible for me to compile the list. Maybe SM64 will be thrown out of the list soon because of Galaxy, and maybe one of the RPG's will be out in a couple of weeks because of Final Fantasy VI. I'm playing this game at the moment and so far, I really enjoy it.

How can I do this?! This is like choosing my favorite son or daughter. You just shouldn't have to.

Faxanadu
Chrono Trigger
Secret of Mana
Silent Hill
Mario Kart