Hmm, I have a bunch of 16 bit games tied at number 1, but if I had to choose one that I played the most and had the most fun . . . probably Legend of the Mystical Ninja on SNES.
favorite classic 16 bit game ... definitely commander keen !! i used to draw out level designs for the game with my friends with all kinds of traps and keys and stuff
I would have to say Secret of Mana on the SNES. I couldn't honestly saw WHY I loved it, just that I did. I went out of my way as a kid to rent it as frequently as possible and to make sure I got the same copy so I could continue my save. When I got older and started working, I purchased a SNES specifically for this game (along with the 3rd person adapter).