It is tough to decide between the NES and SNES. I decided to pick the SNES, since it built on all the 2D work the NES did and continued the Nintendo domination of the time.
After that, I would put the GCN over the N64. While the N64 had some amazing games, so did the GCN. Also, the GCN had a more confortable and durable controller, and had Metroid.
I am very mixed when it comes to the Wii. On the one hand, I love it's innovation. On the other, the motion controls seem so crude that it seems they should have waited another generation before releasing a console with motion controls.
I did not pick the DS since it is a handheld, not a console.