After you get the Megaton Hammer, you can collect upgrades in Death Mountain Crater.
Upgrade Magic Meter
After you land on the Bolero of Fire warp location, go across the broken bridge on the left, then hookshot the broken piece of bridge across the gap, and climb up.
Go to the left and cross the short bridge. There is a cluster of red boulders here. You can't bomb them, but the Megaton Hammer will break them. After you break them, go through the tunnel to reach a Great Fairy Fountain. Play Zelda's Lullaby while standing on the Triforce Symbol, and the Great Fairy will double your magic meter.
Get a Piece of Heart
When you exit the fairy fountain, look to the right to see another red boulder. Use the hammer on it, then jump across, there's a boulder on the ledge to the right that you can hammer out of the way. From that ledge you can jump across and climb the ladder. If you turn to face the entrance of the Fire Temple from here, you can climb down the wall to reach an alcove with a piece of heart in it.
Get a Gold Skulltula
Climb back up. Go through the tunnel ahead to reach the top of Death Mountain Trail. Climb down to the level where the eruptions used to be, and hammer the first boulder you encounter. Then turn it to night if it isn't already, and a gold skulltula will appear there. Get it.
Get Another Gold Skulltula
Go down to the fence where you threw the bomb flower to open Dodongo's Cavern. Hammer the rock to the right and you find another gold skulltula.