I've always worried about that in the past as well. Especially since having a hurricane flood our house in Maryland years ago, the memories never leave you comfortable.
There's a foaming system that's been around for a few years where they come in and enclose your entire basement rafters and side areas. This means also enclosing all water pipes, gas lines, etc. A neighbor had this done recently for $800 and the sound protection was also super if you are looking to install a theater in the basement.
http://www.greenbearinnovations.com/insulation.html
I'll be doing this soon enough so we can pull all our insulation out and enclose the whole basement ceiling. Just trying to figure out how much work this is going to be taking everything out so they can do the work, or can they just work around the comic racks if I cover everything in plastic.