I can't sleep at night if my tools aren't back in the right place. I don't have a ton of them, but I have what I need to be fairly efficient at most jobs. Part of that efficiency is organization. If I'm in the middle of a job and I haven't used a tool in a while, I'll put it back in its spot in the box. I can't stand to work in a cluttered area. This probably comes from my time and training in professional kitchens - I'm a huge proponent of 'clean as you go.'
Not to mention, the act of cleaning up helps me reorganize my mind a bit. If I get stuck on something, I take a break to straighten up and shift the problem back into my subconscious while I 'concentrate' on cleaning. As I'm putting stuff away and not focusing on the problem, I'll usually come up with at least another way to tackle it as I sort of zone out.
The other thing is that having a place for everything in the box makes it easy to see what's missing. With a pile of sockets in a drawer, you can't very easily tell if your 10mm 1/4" is missing (it probably is, and it's probably still on the short extension in your back pocket, if you're anything like me).
But, there's no right way to organize. What works for me won't work for everybody. The downfall of my system of organization is that if something's not in its place, or in another typical hiding spot (1/4" flex head ratchet with short extension and 10mm socket hanging out of back pocket), I'm clueless, and I'm screwed until I turn everything upside down to find it. Most of the time, guys with jumbles of tools have a near-photographic memory about what tool is where in the jumble. They can reach in the haystack and pull out the needle just about blindfolded. But, move that needle a foot to the left before they have a chance to look again, and that thing is gone.
I wrenched at a motorcycle shop with a very good friend for a couple years, and at first, he and I would almost come to blows over tool organization if we were helping out on each others' lifts. He's a MESS while he's working, and it drove me up a wall. But my insistence on organization (and I'll concede that it's easy for me to take it too far) did the same to him. After a while we got over it and just learned to laugh at our habits.
As far as tool organization goes, I really only have a few specialized devices. I love these socket organizers, because the socket only fits on the correct-size post, and the size is easy to see at a glance.
I used this cheapo wrench organizer, which I cut up to better fit into my drawer:
Screwdrivers live in the tray in which they came:
Beyond that, everything just kind of has its own spot in a drawer. I'll post up some pictures later on if anybody really wants to see them, but I imagine my organizational habits aren't terribly enthralling to anyone who's got this far in a surprisingly in-depth reply to a rather innocent question.