Gamecube, hands down.
Why? Because of the sheer level of quality of it's best titles.
I'll grant that the SNES and N64 had more quality titles. Having had both during my formative years, I recognize the impact both had on me and the industry. I loved the hell out of them. I still have working versions of each and vividly recall fond memories of many a late night sleepover playing games like Goldeneye, Lemmings, Wipeout64, Conker's Bad Fur Day, etc, with friends.
However, that said, I would pit the likes of Metroid Prime, Mario Sunshine, The Legend of Zelda: Windwaker, et al, against the best either the SNES or N64 had to offer. And, for me, I find myself pointing more frequently towards the titles on the Gamecube as examples of game-design masterworks than I do titles on the SNES or N64.