[hounddogs!]

Good to see I'm not the only neurotic one...

Hole saws definitely go with drill bits. My rule is that the tool or consumable goes with the driver.

Hole saws and drill bits go with the cordless drill
Boring bits and mixers go with the spade handle drill
Punches and chisels go with the hammers
Wire terminations go with the stripper/crimper


Many things are grouped by task:
Grease gun, filter wrenches, drain pan, filters and oils all live together on a shelf.
Caulk, roof tar and liquid nails all are close to the caulk gun.
Anything welding is on the cart.

For the household stuff, I've taken to using individual small toolboxes for copper plumbing, electrical, black iron plumbing etc.

Keep improving. I've had three different garage layouts in seven years here.