Stage Select:
1. Unlocking Cloud in Final Fantasy Tactics.
2. "ZELDA" in the original Zelda, which allowed you to skip to the Second Quest.
3. A subtle but memorable one, for me at least: In Tales of Symphonia, in the slums of Meltokio, you'll run across a girl selling flowers. My favorite Tales game references my favorite Final Fantasy game.
Pak Watch: Metroid
At the time, it was almost as amazing as The Legend of Zelda on the NES. The huge world, the multiple power-ups that unlocked more of that world, the secret passages, and the hunt for the bosses, Kraid and Ridley, even if Ridley wasn't as impressive as his later incarnations. Kraid, though, was actually much harder on the NES than he was on the SNES or GBA. The music was some of the best on the NES, especially Kraid's Lair, Norfair, and Ridley's Lair. Once I finished Zelda, I went into Metroid whole hog. Unfortunately, compared to Super Mario Bros or The Legend of Zelda, it's probably the least playable of those NES classics today. So many massive improvements were made to Metroid's graphics, sound, game mechanics, and controls on newer hardware, that it feels primitive and clunky by comparison. Super Metroid alone rendered Metroid obsolete, and its GBA remake, Zero Mission, renders the original game somewhat pointless. Still, it was a groundbreaking game and deserves to be recognized as such.