No matter what you do, at least keep all the important stuff on the same floor. It gets really, really tedious if you have to run up and down stairs all the time to get stuff done. I keep my depot, ore processing line and workshop in the same hall, with my bed in an adjacent room. The hall has large, open windows so I can enter or leave in any direction via jetpack. Below it is an infrastructure floor, with power cables strung about. It's not a pretty place, but putting all the cables and pipes there really cleans up the main floor.
Even further below is a "rarely used utilities" room. A library with an enchantment table. A chest with emergency stuff in case I die and/or the base runs out of power (in my case, this means a spare jetpack, good armour and weaponry, food, spare tools and a few fully charged Lapotron Crystals to backup the EU system in case the solar panels go bust). My Molecular Assembly Chamber is also stashed away down there, as well as the base's Chunk Loader. I rarely use these rooms, but they are essential when needed (kinda like seat belts in cars), so I keep them easily accessible from my main base.
I guess I should also add a train station soon, when my "1000-metre-railroad" project gets off the ground.