Set up your workbench opposite your bike repair stand, so you stand between them when working on a bike. I've moved my bench and stand around alot trying to get it right, and this definitely works the best (surprise! this is how the LBS is set up too).

I second the motion for a small rolling cart or tool chest, maybe the height of a stool, that you can position near your stand for small parts, holding old baking pans to catch fork oil, etc.

Your workbench top shouldn't be too deep, otherwise reaching for hanging tools can get annoying (if you use tool drawers, this is not really a consideration). Make sure you can get to the backside of any bike in your stand easily.

Leave a clear path from your stand to the door, and from your bike storage to the door, otherwise you'll end up being annoyed every time you want to take a bike out to ride. Sink, outlets, lights, phone, radio are all good things.