Regarding MystCraft worlds with Dense Ores on, you can avoid most of the problems of instability with those worlds by using the Cave World symbol. Unless you dig really far up (y-level <100 or so), you've always got a natural roof over your head. Plonk a quarry down there, hook it to a redstone energy cell (output at 5 MJ/t works fairly quickly, for me), put a chest (preferably gold or diamond, for extra capacity) on top to act as a buffer, and pipe your stuff back home with a pair of ender chests.
That's the method I use, and I get a lot of materials fairly quickly. However, I would suggest using something a bit more powerful than a redstone engine when you're piping things from your ender chest at home to your storage area(s). Even with a redstone engine on the quarry buffer, you can hit an overflow occasionally in the ender chest, which gets really messy, really fast, with BC pipes. If you got the resources, combining a Stirling engine with an autarchic gate (if items in inventory, use energy pulser) works at a reasonable speed, at home, and overflow chance is pretty much nil.
But, really, the best way to mine is whatever way best suits you. Some people prefer quarries, others prefer turtles, others prefer to go down into the depths and dig things out themselves. Experiment, find what works best for you, and just use that.