First of all, the extra buildcraft pipes link has been actualized to a new one that has working versions for both BC 1.7.3 and 2.0.1.
So, as promised, I refined my idea of using buildcraft to make a self-sustaining, almost fully automated tree farm. Why semi-automated? Well, you need to use two levers (one for planting, and one for harvesting once the trees have all grown), and I didn't made any self-fueling circuit for the machines (since those take a lot of space). The only problem with this contraption is that using steam engines (the coal-powered ones made with stone) means you need to harvest and replace the engines of the fillers after each harvesting, because they overheat very quickly when powering a filler in clearing configuration.
So how does this work? First, I made the farm, in this case a 17x17 hole (plus the borders made with wood, taking an additional 2x2), and filled it with water currents (two rows going in the direction of the pipe system, then a current going from each side to the center where the obsidian pipe is), then I made the "placing template" you can see to the left of the screenshots, then the pipe system and finally I placed the machines, engines and cables.
The operation of the contraption is quite simple: activate the builders to place the dirt and plant the trees over it (in the screenshots we can see this already done), wait for the trees to grow, then activate the fillers (you can use one filler only if you prefer, but it will take much more time), and when all is cleared, repeat the process.
Of course, nothing prevents you from making a much bigger version of the contraption, up to the 64x64 or so that the land marks reach (or if you use several builders...), however that might cause a lot of lag from the huge amount of water currents. Adding a clock and a toggle latch to the circuits can, after calculating the timing, turn off the fillers and start the planting process, and limiting the amount of fuel in each engine to the minimun to perform their duty (in the case of the engines powering the fillers, at least) is a good idea.
Without more delay, here is the video of the contraption at work:
Oh, I didn't used a quarry, but with a RedPower's circuit with a clock, it can be made without much fear of over-digging (sadly, my quarry tends to keep powered after the engines have been turned off...), or once you made enough holes till the bottom of the map, you can make the farms down there.