I have a 20x24 shop buit onto my home just for model building. After 37 years or so of building planes I have developed a few ideas that might help others. I too looked at the other threads with interest, as I am somewhat a shop junkie anyway. The re-occuring theme is always not enough space and half finished airplanes are sitting around getting dinged and/or forgotten. I am certianly guilty of this myself frequently, and even with my big shop I still damage my projects with hangar rash.
My main interests are large scale planes. These take up a lot of storage room after they are built. My main fault in designing my shop is not designing a dedicated area for storage. I have resorted to storing my finished planes in my RV outside.
As far as workbenches go, each person has their own ideal bench design in their head. I went through several designs over the years and noted the advantages and disadvantges and I have finally came up with my ideal bench. (for now anyway

) I have perimeter benches running around the exterior walls that serve as building stations. An example would be a pin board area, a saw/sander/drill press area, electrical soldering area, etc. I feel that it is important to get these benches dead flat and level for accurate building. Take your time here when constructing.
I have a large 4x8 island bench in the middle of the shop that serves as the main assembly area and a general catch all area. On large planes I find it VERY helpful to be able to walk around the plane to build and especially for eyeballing dihedral angles and such. I also have a dedicated electrical service to the shop room. I have outlets placed every 3 feet around the entire room and also incorporated into the main center bench, for a total of 62 outlets! Believe me they all get used too.
Sanding dust currently goes everywhere till I build a downdraft sanding box. The electrical assembly area has it's own 12v power supply setup that I copied from my club field charging bench. I can charge several batteries at once and my soldering station has all the necessary supplies at hand such as solder, flux, shrink tubing and the like. I have a small cheap moveable vice to hold hot things and use a small piece of tile as a heak sink. Hardware storage is an issue that I have yet to resolve. Plane parts come in all shapes and sizes and can take up a lot of valuable shop real estate fast. I'm still looking for ideas in that department.
My shop is heated and cooled via the house air conditioning system. I do infiltrate the house with dope fumes occasionally which I rather enjoy anyway. Wifey has learned to enjoy it also or so I am told. The only problem is that we can't remember each other's names anymore....
One other issue of must have's is an exterior door if possible. I thank myself each time I carry a large plane out to my landing strip here at the ranch. Being able to fully assemble a plane in the comfort of your own shop and then just walk out and fly is a luxury that I am very grateful for. But just having a exterior door is very important. I hope these tips help a few!