If you bought CDs through your broker, you may want to read this article. It says that when issuing bank goes under, bank CDs bought through a broker (1) stop paying interest (2) funds are not available (3) need to ask your broker to file paperwork with FDIC to be sure that you recover your funds (same limits apply as at the bank)
P.S. Sorry... Yahoo! won't let me post the link.
It's from USA Today under Money. The article is dated July 14, 2008 and talks about FDIC insurance coverage at IndyMac. This is information that I've not seen other places.