(i used diamond pipes in the beginning to do a quick sort at the dig site and seperate cobble, dirt, gravel,... from all the useful materials...
You can do it with itemducts without any filtering setup: quarry -> vanilla chest on top-> itemduct with servo sucking out, and a series of DSUs (cobble, gravel, dirt, sand?, marble?) than a series of chests (diamond?) or an ender chest.
Just don't go with corners on the itemducts.... Trust me.
Back on the topic: I read somewhere about a script for turtles with mining just the good stuff and replace it with something else. Just as quick as a quarry.
Personally I put my cobble where it came from (filler from buildcraft) and a nice layer of dirt on top (my entire island looks like a flatland).