My job was in limbo while I was applying, and I wasn't "best friends" with my newest boss. He had been given our terrirtory to manage in addition to his regular area in order to keep HIS job, so he wasn't exactly thrilled about meeting all of us. Needless to say I wasn't sure what in the hell he'd say about me if the Navy started digging into my employment references.
So my solution was to list my employer on my app, but I included in my application, a form letter that asked the board not to contact my current employer. It is a pretty standard procedure according to my recruiter.
Sooo, you figure out what all you can do with that, but be warned that the security clearance people can speak with every employer you've had in the past 7-10 years, and they will want you to explain any gaps in employment. Then again, getting laid off wouldn't be detrimental to your sec. clearance, and it is commonly completed after the boards anyway.