Best way to mine is Using RP frame machines. Takes a long time to set up, but it eats away the earth at a faster rate then a quarry. If you don't want holes in the world. build the RP machine under the surface of the earth OR make a deploy module on the RP machine to deploy dirt/cobble over the hole.
Like any way of mining in a larger scale, you NEED a way to sort the ore/dirt. Redpower, BC piping will do this for you. You just need to put in the work.
RP2 Frame machine + IC² Miner (with some green gens, or geogen using pumped lava ^^) --> Easy to setup (at least if you've an horizontal area, with planned direction etc ...) and with the IC² Miner efficiency: the cool thing is that you don't have to move it all the time.
Best way to mine is Using RP frame machines. Takes a long time to set up, but it eats away the earth at a faster rate then a quarry. If you don't want holes in the world. build the RP machine under the surface of the earth OR make a deploy module on the RP machine to deploy dirt/cobble over the hole.
Like any way of mining in a larger scale, you NEED a way to sort the ore/dirt. Redpower, BC piping will do this for you. You just need to put in the work.
I am currently sitting in my first larger attempt of such a machine and it works pretty fine. It clears about 81 blocks (9x9) at bedrock level every 3 seconds, throws all excess cobble, dirt and other stuff into a lava block, smelts all incoming ore and puts the results and remaining blocks in the chests. Effectively all I have to do is to stay here and wait for the resources to come in. 2500 blocks so far and continuing. 
The downside was the setup. Ignoring the time it took to actually prototype and research all those things and how to build them, it still took about 2 days (~10h) to actually set this thing up to get the setup that is now running underground. People with less experience in building those things might go crazy at some point. An IC2 miner is not that convenient but can be setup a lot faster.
Supporting the thread necro, but I notice no-one's mentioned that you can always set up a quarry at sub-ground level, to minimise how much mining of basic dirt/cobblestone you need to do. If you're after the higher value ores it can save some time (although personally I just used to funnel the useles ores into recyclers, which I figure is pretty de rigeur).
I've now moved to CC Turtles though - fine-tuning my code, but I have them dig straight down to bedrock and then work their way up. Prioritises the valuable ores, and I can set a ceiling on them at which point they end their cycle and return to the surface, calling it a day. Saves mining the top-soil if you're not after the basic ores. I know it's not IC, but worth considering for some maybe. Otherwise, quarries were always my favourite (and the mining laser)...
Idk what you guys say, so long as you can evade the debuff, nuke mining is still more fun 
This http://www.youtube.com/watch?v…U&list=PLF2795ED195FA49E8
~25 min into the video
I haven't built it yet but given the change to ore gen with TE installed and the requirement to mine at at least 2 levels (no tin or copper under 35, so you have to high mine as well as strip at 16 or less) I'm going to use a Frame TunnelBore\IC2 miner hybrid bastard, I figure a pair of IC2 miners (with Diamond\OV) setup on a frame tunnel bore, 12w9h head, at 40ish, will give me all the tin\copper I'll ever need as well as mining out a nice 18x9 area to bedrock on each stop (for diamonds\nicolite\redstone etc) also it'll be fun to build 
Sidenote, Arcane Bores on frames were stupidly good. I had one that would in minutes strip a 25ish wide area to bedrock from y=64 then move forward 5 and do it again, it literally(and I do use that in it's proper sense) ate strips of the world.
List of Mining Tech in My Current World, its about 1 week old.
1. Wood Pic
2. Stone Pick
3.Iron Pic
4. RedPower2 Gem Pick
5. ComputerCraft Mining Turtle
6. 3 Diamond Picks (1.Fortune 2.Silk Touch 3.Unbreaking)
7. RedPower 2 TBM
#7 is a WIP, as I need some tech first, the list is as follows.
EnderChests for Transport of Batteries and Raw Resources
Sorting Machines & Tubes for Processing Resources
IC2 machines for Processing, plus the power needed to run all of these
Extra Dimensional Barrel Upgrades for Storing 1024 stacks of stuff like copper and tin ingots
Lots more Blutric Power, as all my current power is used to fuel an automatic stone brick maker, and my tree farm that provides fuel for my turtles.
I play with GregTech with all hard settings enabled, so its rather tough to get stuff like blaze rods, and macerators.
I would say that having 2 or 3 mining turtles digging from layer 16 to layer 5 is much better than mining by hand, even with max fortune enchant. They dig out a 64x64 area each, so I dig out roughly 120k items and blocks per run. Usually nets me about 24 diamonds per turtle, per run. Each run takes about 2 hours, so I get half a stack of diamonds every hour, and the system is totally automated using GPS, when they got low on fuel, they pull out an EnderChest, grab fuel. They dump their items into another EnderChest, which is pulled from using a filter, into barrels and chests. Cobble, and sand are both voided.
I just AFK overnight, I have never gotten this many resources before in a world.
The other, more important question is: what is more fun?
I for myself love the Red Power TBM for a very simple reason: I never had so much fun building one. Placing down an IC2 miner is probably more efficient, but it is at the same time plain boring.
Hmm, for manual mining for me it is
Wooden Pick --> Stone Pick --> Iron Pick (or Bronze if short on Iron) --> Ruby Pick --> Nether --> Diamond Drill + Rockcutter --> Fortune III Pick --> Imma Firing Ma Lazor
Have to say I was lucky today, managed to get a Fortune 3 on a pick on my first try (30 levels).
i go for frame quarries but until then I mine by hand assisted by a quarry. :3
Frame tbm is the best by far. You can always add more blockbreakers
Frame tbm is the best by far. You can always add more blockbreakers
There is only one problem with that and that is power supply. Unless you use other addons to convert power, you cannot supply huge TBMs with enough power to run constantly.
You could build one row of Block Breakers that goes up to say Level 80 and makes Space for the Sun.
It depends on what I'm after. A miner gets me crazy amounts of copper and iron, a consistent uranium supply, and a decent amount of tin. For diamond redstone, lava, or even more tin, mining by hand works better cause I can just branch mine down at layer 10
Frame quarries are definitely the fastest way though are fairly expensive to build all the frames seen as you will need a lot of brass but aside from that you can set up an automated battery filling system that will last practically forever using ender chests a filter and a retriever on the quarry end and then another ender chest filter and retriever attached to a battery box probably with a windmill powering it and that will go forever, just don't do what I did and lose your only way of getting to it short of a 6000 block walk by dying in lava. However the one thing to be aware of there is if you build one at like y = 6 or so you will get a lot of diamonds, iron, redstone and nikolite but no copper or tin if you use TE ore generation which anyone using most of the packs in the FTB pack will be.
Currently branch mining for redstone at height 11 with diamond jack hammer+silktouch diamond pickaxe+advanced diamond drill, pretty good.. get around 2-3 stacks of redstone ores per hour.
Me jelly. I lost my old world due to carelessness. Don't mine straight down. I learned that the hard way. Of course I was carrying every piece of IC2 and GregTech stuff I had. I then landed in a cave and breathed a sigh of relieve when I remembered my rubber boots kept away the ladies and fall damage. Then some ass of a spider pushes me into lava, and I could not jetpack to water fast enough. I was so pissed, I just deleted the world and started fresh, not worth it trying to get all my stuff again. (That of course flew into the lava)
You might ask, "WTF Would You Carry All That Stuff On You!". I was moving my base to bedrock, to protect it from my little brother that enjoys nukes.
Short Story: Carry water bucket when moving base to protect from nuke happy family members.
I mine by hand. I mix enchanted tools with powered tools so I can use a rock cutter to mine the ores, or a drill if it's safe to mine, a jackhammer to clear stone, and a fortune pickaxe to increase ore drops in the end. I don't have a enchanted pick yet, so I usually just store it all in chests and use only what I need to build my needed tools.
While this is slower and can't get me everything, I prefer this method because I like caving. I enjoy fighting off foes while looking for rare stuff, sometimes finding chests full of rare loot, usually finding string, redstone, and a saddle. But in the end, I prefer it this way. I find all kinds of neat things that I wouldn't if I just set a quarry to mine, or used a frame mining setup.
Though I do plan on building a big Frame Base, one which has a ton of storage space and has IC2 miners set up to mine when I want them to, sorting everything into it's place in the storage rooms. I plan on using Magic Engines with GregTech to power the IC2 stuff. I wish Redpower had a way to convert other mods power into Bluelectricty. Then I could power the whole thing with them.
