Seems like a plausible idea but it would still have to be separate carts. The N64 library wasn't a huge library of games to begin with, just to think:
Nintendo - most of their first party stuff could show up here, many are still waiting on a re-release of DK64, A GX looking F-Zero X would be super sweet (with some added DLC tracks), Majora's Mask has already been hinted at, would LOVE a remastering of The New Tetris, all the other Rareware games are a no-go, sadly.
Konami - I'd gladly take a 3D remake of Legacy of Darkness, I actually enjoyed that game.
Capcom - Not much here, we already know the deal with MML, and people have been begging for an RE2 remake for years.
Lucasarts - All their Star Wars games could be brought back in a big way here, with standard 3D imagine seeing definitive versions of Shadows of the Empire, Rogue Squadron and Episode I: Racer, would be sweet!
Midway (now WB Games) bring back Mortal Kombat Trilogy and Mortal Kombat 4, remastered for online play, just might be the thing to pull me away from SSFIV and DOA! :P
Can't really think of much else, but THIS is what I personally would like to see from N64 brought back for 3DS. --- [3DS FC: 0645-5794-3020] [GE007 FC: 1237-3974-3165] [COD: BO FC: 2463-7578-3340] [TvC: UAS FC: 2923-0604-8719] [SW3 FC: 0045-9248-8653]