As far as my gameplay goes, my sorting system goes like this: pile everything into as few chests as possible (so I don't waste any wood), and then don't do anything but mine with that pickaxe for the materials needed to make an Applied Energistics system - an ME Controller, a Terminal, and a Drive. And then make at least 2 of the 1K drives. Once I have that made, I never ever have to worry about pipes or sorting or anything (only worry about power, so Thermal Expansion is a close second in importance during this phase of my gameplay).
tl;dr: AE for all my sorting, as soon as I can possibly get it up and running (very early game if you focus). AE can sort by how many items you have, or it can sort by alphabetical order, etc. It's the best mod ever if you hate clutter and having a bazillion chests scattered all over!!