The bottle, from the Legend of Zelda. So simple, yet it's probably one of the most useful items in the game.
The airship, from a lot of Final Fantasy games. Not sure if it counts as an item, but it's still really sweet when you finally get it. You feel like the world is your oyster, ya know?
The arm cannon upgrade, from any entry in the Mega Man X series. There are generally four capsules to find in each game; an armor upgrade, a helmet upgrade, a speed upgrade, and a firepower upgrade... But we all know that the most sought after is that last one. Aside from giving you the power to charge your enemy's stolen weapons, it lets you plow through smaller enemies that might have otherwise taken a while.