I am actually going through this same issue right now, so I can't help much. I'm actually tearing down my existing base and rebuilding with a bit more purpose and planning. The gregtech multiblock machines are huge. a 3x3 for the base, then a control machine on the outside (5x5 if you run all 4 faces), and you have multiple multiblock machines if you build them all.
You will need space for a IC2 power room, buildcraft power, along with the wiring, piping and any automation. Railcraft iron tanks for liquid storage. Logistic pipes are fairly tight space wise, but RP2 automation can get rather involved with space needs.
Look the the power room and base picture threads. Maybe you will be inspired. Aura nodes exist in the twilight forest now, so maybe build a base inside one of the huge trees.