OK so this is a kinda old post but....
I had the same idea in mind, create an install disc with just sp2 and hot fix`s and then have a seperate disc for apps to be installed at a later date.
I quickly gave up trying to run a cmd batch file with autorun, what i did was got a hold of a batch compiler (Batch File Compiler v5.1 to be exact) took my cmd batch and turned it into a .exe which of course runs just fine with auto run.
Only down side is the EU interface is kinda blah, anyone know a better way to set this up?
I tried using cmdow for my interface but didnt get anywhere with that.
If anyone wants to "lend" me their installer shield configurer that might be quite nice

Then make an istaller that allows a choice of what apps to install
Outside of buying installershield for about $1,000,000 i have no idea how to improve on the EU interface.