So I've decided to upgrade the main panel to 200 Amp service and have a sub-panel run to the garage. My garage walls are just the studs so running the new electrical will be easy. What recommendations do people have as I might as well have the electricians do as much of the work as they can while they are here.
Any 240V machines need their own specific solutions. Until you/we know exactly what those machines are (or will be), it's pointless to guess at it further.
For your general-purpose 120V outlets, my usual "recipe" will likely suffice: Put one double-gang box every 6-8 feet around the entire perimeter of the space, with each of the two duplexes in that box fed from a different breaker than the other one. In small shops (such as yours), two 20A circuits will normally handle the whole thing; in larger shops, split it up further as you see fit. Optionally, add a third circuit in the vicinity of the workbench, especially if you (will) have high-draw tools (bench grinder, drill press, etc.) in that area. Keep the bottom of the boxes at least 49-50 inches off the floor; you'll understand why the first time you try to store a 4x8 sheet of plywood, drywall, etc. And finally, note that at least in anything which might be considered a "residential garage", NEC now requires that ALL 120V outlets be GFCI protected.
For the general lighting, it largely depends on the specifics of the space (i.e., the dimensions, most notably including the ceiling height; the layout of the work areas; the interior finishing; & etc.) and what sort of work you will be doing in there. Typically, you'll want three switch loops: One for walk-through lighting, and two for the "Main" lighting. The lighting should be split between at least two separate circuits, so that if/when one trips (or must be shut down for maintenance), you're not left near-completely in the dark. At least the "walk-through" lights (and ideally, ALL of the lighting) should be controllable from EVERY possible entry point.
Your workbench and any permanently installed machinery will also require suitable task lighting. One or two outlets in the ceiling for such things as trouble lights on retractable cord reels is a reasonable idea. But otherwise, any fluorescent lighting should be hard-wired, so as to avoid the need for running it from (now NEC-mandated) GFCI-protected outlets, which is often a problematic combination.
If your overhead garage door(s) has/have torsion-type counterbalance springs (or can be retrofitted with such), then a side-mount opener such as the LiftMaster 8500 will make for a MUCH neater, cleaner installation, without a belt/chain track cluttering up the center of the ceiling:
http://www.liftmaster.com/lmcv2/productdetail/19724/liftmaster-products/
To be much more specific, we'd need to know more about the details of the space.