As long as the builder doesn't quote something crazy for the 100A sub panel, this is the way I'm going to go.Have the builder put in a 60amp sub panel and then do the rest later in exposed conduit. That way you can calmly plan what you need/want. With a little guidance, wiring isn't a big deal. Homeowners can typically pull their own permits and do their own wiring.
A 100 amp sub panel might be better just from the standpoint it will hold more breakers. Cost will depend a lot on how far the sub is from the main disconnect panel.
What you don't want to do is have all your shop lighting fed from the sub panel. If the main breaker to/in the sub ever trips your lights will also go out if fed from the sub.
The image below shows where the main panel is (about 6 feet to the left of the arrow) in relation to the new panel, with the proposed 110V 20A and 220V 20A and 30A outlets.
I'll run some PVC conduit (http://www.homedepot.com/p/1-in-x-10-ft-PVC-Schedule-40-Conduit-67462/202295893) from the top of the 100A sub panel over the windows and down to the outlets.
From what I've read, it is permissible to run 110 and 220 branch circuits in the same conduit, as long as the total number of wires doesn't exceed the limits in this table: http://www.constructionmonkey.com/calculations/electrical/tables/wireconduit
I could use EMT but it's a lot harder to work with and I don't need the additional protection.
The lighting, etc. are all on different circuits so no worries there.
Thanks again to everyone for the input.