I tend to use both of them. The only problem i've been having with the OreQuarry program, is lost turtles. The author released a version that uses a pathfinding program that stores every move the turtle made up until the point where the turtle's computer restarted for whatever reason, and resumes the operation from that point forward, but it's not perfect. The turtles often get lost when chunks get unloaded, server crashes, etc... If i was better at LUA, i'd integrate GPS functionality by using Rednet, then it would be solved for good, but the code is so darn big, i can't really make it any better ;(I have two I really think are above and beyond the call of normal.
OreQuarry is just beyond abusively cool. Place down turtle, put a chest behind it for it to fill up, put a chest to its left for fuel. Put smooth stone in slot 1, dirt in 2, chest in 15, charcoal in 16, then run the program. Program tells you what to give it and away ya go. Darn thing burrows down to bedrock and comes back with diamonds first, then as it comes up the levels to your feet it brings in the more and more common ores found higher up.
UltimateWoodChopper is just so worthy of looking up. Heck, if you want to use Sulphur goo instead of bone meal, it can run until you turn it off. Excellent menus, self building, efficient. If it weren't for the fact that I love chocolate so much, this program would make me thinner.