Mario 64. As hard as it is for me to choose something over Paper Mario: Thousand Year Door, Super Mario World, Super Mario World 2: Yoshi's Island, and Super Mario Bros. 3, the first 3D title stands out the most. It was the first true leap in gaming that I experienced in my lifetime, and as such, it will always be the most memorable. Playing it on Christmas morning with friends and family huddled around the television was joyous.
Favorite enemy is hard to decide on. I give Bowser props for the incessant attempts at being a jerk. But I really dig Count Bleck, to say nothing of the wide assortment of underlings from the entire Mario universe. Wario is also an excellent choice. I guess overall I still have to go with Bowser. There's just something so fun about being able to play as him in Thousand Year Door that makes it all worthwhile. Magikoopas deserve a nod as well.
Good luck everyone, and thanks OP!