Bombs?

you get them at Windfall from the Pirates.

go to Windfall after going to Greatfish and seeing the destruction (if you manage to get to greatfish before Ganon gets ther, its still destroyed sadly).

now if you try to go to the Bomb Shop youre not allowed in cuz of the Pirates but thats ok. go around back of the Bomb Shop by Sidling all the way across then cllimb up the vines on the wall and through the hole. this will trigger a cut scene.

when Tetra leaves pay close attention to Mako and Gonzo cuz you have to spell the password right including punctuation and Capitals (if its Swabbies then swabbies, SWABBIES, and any other variation will not work).

now go to the cliff where Tott is usually dacing and you learn Song of Passing. jump off the cliff and onto the deck of the Pirate Ship and try to go into the door. giv Neko the password and cross the room.

this time its harder though. you have the same amount of time but at the other side, thers a gate that closes in front of the door. and furthermore, you have to swing from rope to rope without the little landings. this will take a while.

when you finally get across, Neko reveals that he himself has not completed his own test (I always close the gate on him as I leav for that) and givs you the bombs.

hope I helped

I, too, got stuck after depleting my store of bombs from the pirates. You need to go back to Windfall Island and find patches of flowers. Use your sword to cut them down. At worst you will get rupees. At best you will get more bombs (5 at a time). The patches of flowers are in the large meadow between the town and the bomb shop (near the cliff) and behind the bomb shop itself. After you have mowed down the flowers, just go into any building and go back out again. The flowers will have regenerated and you can try for more bombs. They won't always be there, maybe about every 2-3 times. Be patient, and pretty soon you will have replenished your bomb supply.