I know when my space has got a little bit too crowded, when I turn a model around to view it from another angle and a whole load of stuff gets knocked over sideways and cascades onto the floor. Usually it's the glue bottle, the white spirit or turps bottle or a piece of model that's still setting or drying, tools, tea cup - you name it. The space under my bench is stuffed full of parts bins/greeblie bins/donor household bits and pieces so there's nowhere to 'hide' stuff either.
I reckon shelves above the bench are a great help. Stuff like storage boxes, glues and paints, ref' books can go on the shelves while tools can hang on hooks along the edges or down the sides of the shelves.
Funny thing is, after the best part of 20 years without a modelling den of any sort to call my own...I love it even when it's messy! ;D