Yes, with bees, which is the intended way... As has been mentioned.
The traits that you're interested in when looking for bees for Tree Breeding are:
Flower Pollination - The faster that trait is, the faster your tree leaves will mutate.
Territory (Area): This area describes the area the bee will pollinate your trees in. (also the area in which they'll detect the proper flowers are planted)
Contrary to popular belief, the trees don't have to be planted right next to each other, they just have to be within the territory of the
same bee that's pollinating the tree you want to crossbreed. Bees also don't detect the trunk of the tree, but the leafs, so even if the trunk is outside the pollination area, if at least some of the leaves are in the pollination area, then the tree will have a chance to mutate.
There was a tree breeding chart floating around... Found it:
http://forum.feed-the-beast.com/threads/tree-breeding-spoilers.7869/
The Maturity trait only affects the speed in which the tree will grow naturally, without the need for bonemeal.
The Sappiness trait is only relevant for trees that produce fruit, and it increases the amount of fruit produced when the tree is
harvested in an orchard.
So far, the only unique products i know of, are Walnuts and Chestnuts, produced by the trees of the same name. Walnuts give 0,2 mB of seed oil when squeezed and a 5% chance of mulch, and Chestnuts give 0,22 mB of seed oil when squeezed with the same chance for mulch. BUT, apparently, Chestnuts are produced much faster than Walnuts as well, so that's your go-to source of Seed Oil. If you're into bees, you'll want to get into Tree Breeding and breed yourself a Walnut/Chestnut tree ASAP.
The other woods also have pretty cool looking wood colors, i'd definitely recommend at least Kapok and Baoba. Those two look really, really cool.
EDIT:
Found this in the MCF -> "
Saplings in dungeons was a temporary feature until the tree breeding system was fully implemented - you have to breed your trees to get different types now"