This is REALLY tough...
I've been a Nintendo supporter from the Game & Watch days, and have always appreciated the quality of everything they put out. NES was head and shoulders above everything else at the time, and the SNES > Genesis (IMO). However, the N64 and Gamecube only had a handful of titles that were really system-sellers, while PS1 and PS2 had multiple killer apps and popular franchises. And starting with the Wii/PS3 era there's no contest. Wii lost me as a customer and I have no interest in Nintendo's products going forward. As much as I love the Big N, they've really dropped the ball in recent years.
Ultimately, I give the slight overall edge to Nintendo. The NES was revolutionary, the SNES was great, and even though they had fewer good games, the quality titles on N64 and Gamecube were groundbreaking (Mario 64, OOT, RE4, Metroid Prime). My answer will likely change in a few years, however, if things keep going the way they have been. Nintendo could potentially be out of the console business and most of their best stuff will be 20-30 years old.