Well, if you're not looking to find all of the Skulltulas here (if you are, then check the Skulltulas section), then I've provided you with a very simple walkthrough for the nastiest dungeon/temple in the whole game (the Shadow Temple is right up there with it), the Bottom of the Well.

To open up the passage (as in, drain the water), you must first obtain the Song of Storms as an adult, then come back to Kakariko Village as a child. Go into the Windmill, and play the Song of Storms for the man. The well should dry up.
Upon entering the Well, you will have to defeat the Giant Skulltula guarding your passageway. After that, it may appear to be a dead end, but it is, in fact, a fake wall. Walk through the wall, and turn right (remember, I'm only giving a walkthrough for getting the Lens of Truth, NOT Skulltulas, maps, compasses, etc., because I don't think you need the dungeon items). To make your passage easier, defeat the Green Bubble that circles the path.
Follow the "stream" (while being careful not to fall into invisible holes) until you come to a Triforce symbol. If you've beaten the Water Temple already, then you know to play Zelda's Lullaby to drain the water. Now, go back to the beginning after you get past the fake wall. The little nook that was previously filled with water is now the passageway to the Boss! Grab the bombs out of the chest, then proceed to crawl through the hole. Defeat the Giant Skulltula guarding the path, then open the door to the Boss.

The Dead Hand is the Boss of this mini-dungeon (and the Mini-Boss of the Shadow Temple). When you enter his lair, you'll see about ten red and white arms protruding through the ground. Watch out for these during your battle, but you'll also be using these to lure out the Dead Hand. The hands can be destroyed by Din's Fire or Sword Slash. Either way, you must get caught by one to lure out the Boss. When you do get caught, press any of the buttons repeatedly to get free, or he'll bite you. To kill the actual Boss, I prefer using Din's Fire, depending on how much magic you can carry, and sword slashes work nicely, but just about anything works against him. Once he's defeated, a big chest appears, holding the treasure of the dungeon: The Lens of Truth!

Note: If you use the Lens of Truth and look behind the big chest, you'll find an invisible small chest! This item is also important for use in the Shadow Temple, Spirit Temple, Ganon's Castle, and finding Skulltulas in this mini-dungeon.