Yeah, 3D has been attempted on lots of video game related stuff (Famicom and Sega Master System with shutter glasses, Vectrex with the 3D color wheel, etc)… but typically it was an add-on, only used for a small set of games.
The VB was the first “3D only” gaming console that I know of… and I think that’s what the big deal about the 3DS is. Rather than just being a cool add-on with limited support… they’re pushing 3D as the main feature.
I believe they just need the standard red/blue anaglyph glasses. AFAIK the NES never had any actual 3D peripheral hardware like the Famicom’s shutter glasses.
Depending on your TV, color settings, etc… you may want to try both red/blue and red/cyan to find which works best for you.