At some point I stopped believing in Top 100 lists because the top winners keep changing (you'd expect an old game to remain near a certain spot, but just in those two examples, #1 changed between Super Mario Bros. and Super Mario 64), the list would be subjective anyway, and it's not clear what makes a game Top 100 material. Is it how much of an impact it had on the video game industry? Is it how fun and replayable the game is after all these years? Is it whatever games are Napoleon-Dynamite-style sweet at the time (like Halo 3)?
Sure, I make lists for which games are my favorites, but I could never bring myself to do a Top 100 list. I read the lists more to see if my favorite games appeared. Hence my joy to see Okami and Secret of Mana on the most recent list. Sure, Mario might have the most influential games of all time, but they don't rank as the most fun games for me to play today. I couldn't care less about Super Mario Bros. or Super Mario 64 at this point. Where was Banjo-Kazooie on the list, if it was there at all?
By going with my definition of favorite game for Top 100, what I'd call the best game of all time is Secret of Mana. It's not perfect, but every time I return to it, the atmosphere is such a breath of fresh air, the combat never gets old, the music is timeless.