(Note: When considering Wii and WiiWare, I am not taking into account Virtual Console or Wii's GCN backward compatibility.)
I suppose I'm asking the question from the point of view of: which one has the games you enjoyed most? and why is that system your favorite?
I... am having a tough time with this. But I vote SNES. It was a golden era in gaming history when you had the very best developers from first party AND third party, all creating high quality games on a single platform. I would argue Nintendo has not been able to recover that third-party support to the fullest degree since that era.
Let me confer with X-Pert and some other "old" folk on awesome NES games though! I only did what I had played, and I REEEALLY skimmed it.
Here's one I know I didn't count on my first run simply because I missed it.. --Have you guys (anyone else besides me?) played Space Shuttle Project? Its simple, yet addictive/awesome!, and I don't think its ever been done again (exactly like this, I mean):
As the guy in the video says, it gets harder and harder in missions following, picking up more stages and more things to do per stage.