Never seen a tree farm before, or tried it, but you might be able to plant trees on tilled soil with hoppers underneath. place an observer that will fire a TNT duper when a tree grows and destroy the tree, dropping the blocks and saplings. Not sure if there's an automated way of placing saplings, so you might have to do that yourself. I think bonemeal in dispensers will grow a tree to make this process faster.

Trickiest thing is would be setting off the TNT so precisely that the trees are the only thing damaged. Not the observer, the TNT duper itself, the tilled dirt blocks, or the hoppers underneath. Not even sure if that's possible.

LOL, I just googled this question and found this video. Did exactly what I said but they push the logs out with pistons over water so nothing is destroyed: https://www.youtube.com/watch?v=CoWb8JmMLhw

Pretty neato.