I've 'favorited' the games in my collection here on this site in order, so there's basically a top 40 right there. These are my top 5 games, which is unlikely to ever change. I hold every one of these games in extremely high regard, to me they are as close to perfection in gaming as possible.
#1: The Legend of Zelda: Ocarina of Time (1998, N64)
#2: Star Wars Knights of the Old Republic (2003, PC)
#3: Super Mario 64 (1996, N64)
#4: Super Mario World 2: Yoshi's Island (1995, SNES)
#5: The Legend of Zelda: Link's Awakening (1993, 1998, GB)
Yes, I think Yoshi's Island is vastly superior to Super Mario World in my eyes. I've never understood what's the big deal about that game, Yoshi's Island is underrated. Outside the top 5 is where it gets a little more varied. The top 10 are all excellent games, but it is probably possible for a new game to enter the top 10. Because I live in the PAL region, I sadly missed out on certain time tested classics like Chrono Trigger.
#6: SimCity 4 (2003, PC)
#7: GoldenEye 007 (1997, N64)
#8: Mario Kart 64 (1996, N64)
#9: Super Mario Bros. 3 (1990, NES)
#10: Rollercoaster Tycoon 2 (2003, PC)
As you see, my top 10 is Nintendominant. The rest of my favorite games list becomes a little more multiplatform, but my first non-Nintendo game (besides PC) is not until #12, Soul Calibur on Dreamcast, and Medievil on PS1 at #14.