In spite of all the cool gadgets and high tech firearms that people seem to be displaying across this thread, i have to give my best weapons ever award to something less complicated yet proven to be the most effective tool of its time.
From The Legend of Zelda Wind Waker: Light Arrows
Aquired near the end of Link's quest, the Light Arrow was the only way to proceed throught Ganon's Tower, and the only thing to truly kill Phantom Ganon.
I am telling you, after hours of tedious sword fighting with powerful enemies that, even with the Master Sword, were annoying to fight over and over again, being able to just end their exsistence with a single arrow was more satisfying than any high powered bulky supercharged techy gun from the future.