The .minecraft/redpower/redpower.cfg file contains the block ids for ores (inc. gemstone ores) and stones (marble/etc).
The .minecraft/config/IC2.cfg file contains a line 'valuableOres=' and a list. The list has a format of blockid:value,(space)
The normal minecraft blocks are obvious; the industrial craft blocks IDs are defined in this very same file. All that's missing is telling IndustrialCraft which /other/ blocks to mine for. In my case 140:2, 142:2, was missing.
Hayo! The automated miner does a nice job.
( BTW, if you want it to also get more cobblestone, sandstone, clay, etc, just add the block IDs to that list. This should also work for glowstone and other resources... but I'm not sure if it is able to collect material before it drops/if it is surrounded by lava O.o )
Here is my current line (this will even 'mine' RP2 trees, but that's REALLY costly compared to breaking out a chainsaw!):
valuableOres=14:3, 15:4, 16:1, 21:3, 56:5, 73:3, 144:1, 141:1, 143:1, 140:2, 139:1, 142:1, 247:4, 248:2, 249:2