There are two upgrade fountains. Throw your bow, sword, or other item in and sometimes it will get upgraded. To find the first fountain, remember where the ring of rocks is located in the Dark World. North of there in the Light World is a cave behind a waterfall. Swim there and only throw in your shield or your boomerang. To find the second fountain, on the Pyramid Of Power is a crack in the wall that only a super bomb can break. Use a super bomb to blow a hole in the wall and toss in the tampered sword (Lv. 3 sword only) or your bow. If you toss in items, say that it is yours. Toss in an empty bottle and get a green potion back.