First rule - organise a place for everything then keep everything in its place, even as you work. (Put a tool back in its place as you finish a task with it, rather than on to a bench clutter). As you use them, you'll develop an extensive memory about where they all are and so save all that hunting-for-it time.
Rule Two might be: put everything around the walls and leave yourself a working space in the middle. Not always possible. especially with machines that handle long workpieces .... but it does make the most of space and generally allows you to more easily reach things.
Rule Three might be: put infrequently-used tools packed away in drawers and cupboards whilst keeping frequently used tools instantly gettable. I use magnetic rails and pegboard with various hooks and other holders, with the highest concentration of such on the other side of the bench that I work at.
Pics will follow in due course.
PS I work in a rather small one-car garage.