Zelda. It's close, but Zelda.
I haven't played Skyward Sword or 3D Land yet, so it's pending those two. Recently Mario has been better with Zelda, with the Galaxies being pretty sweet and the DS Zeldas being the only truly bad games in the series to date (with Phantom Hourglass being subpar and Spirit Tracks being f***ing atrocious). Prior to that though Zelda wins by a hair, mostly because it has the superior portable titles in LA and the Oracles. It's pretty close on every other system though. All of the NES games in both series are classics, even SMB2 and Zelda II, the SNES is about the same between LttP and SMW2 for me though I'll take both over SMW, and on the N64 I feel like SM64 hasn't aged as well but it's still good, but OoT has aged fine and MM has arguably gotten better with age.