My reply doesn't deal with the tools or workbenches, etc. you'll need, but I will tell you about some things I did when we built our house. I can honestly say there is nothing I would change about the space.

I don't know how large (small) your budget is, but my shop is right off from a room with a scrub sink where I often wash myself or some part, etc., check for innertube leaks, etc. It's also nice to have a toilet close by. I have heat and an evaporative "swamp" cooler, all of which makes for a great work environment whether it's hot or cold. We also have an intercom out there so my wife can call me for chow.

I painted the floor with two coates of gray epoxy and really am glad I did. It makes for such easy clean up. I also keep some rubber mats under my work areas, so if a part drops, it is less likely to break or roll away. You can purchase this mat material at Lowes by the foot. I made cabinets with doors so everything stays nice and clean no matter how dusty things get. I also do woodworking. My next chore is to finish sand the sheetrock seams and paint all wall and ceiling surfaces. It's a 3-car garage with another dedicated, partially walled-off shop bay, so it equals a 4-car size. It will be a lot of work to prep and paint all of those surfaces. I also have running water in the garage and a floor drain so I can wash my bikes any time of the year. Sometimes I come into the house...