There are two tree's in the same area as the flute guy who wants you to find his flute. In this area in one of the worlds I forget which one but there are two trees next to his other that both have a red rupee in it. Just use your Pegasus Boots. Leave and come back and the rupees will be back every single time. Also the tree near the portal closest to Kakariko Village. You will need the hammer I think. This tree will always contain magic. A Big bottle that will completely refill your magic at any time.

I've played this game many times before and have checked every tree in the Dark World. I have never any items from the trees.

Same Here,Redead Sniffer...
I might try though...Again.

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Well, I'll give it a try. I haven't beaten LttP yet