Is use of multiple bibliographies, especially with annotations, in a thesis, accepted? As I am reviewing sources for my thesis, I am citing my sources in an (APA style) annotated bibliography (as required).  However, I am also finding some excellent points from other sources that are either not entirely on-topic or less-empirical (read: poorly referenced).  I have (of course) kept track of them.

What is the accepted practice for listing cited works in a thesis?  Is it acceptable to have an annotated bibliography, as well as a list of "additonal works cited?"  Or should they all be listed (with annotations) consistently in one section?

I have posed this question to my adviser, but I would also like to hear from others as well.
I think the answer to your question is very dependent on your subject and the culture of that research area.  In my area, math, I've never seen an annotated bibliography as part of the thesis.  I've probably only looked at 15 or 20 theses, but I've never seen one.  In other areas (humanities and social sciences?), I suspect such a bibliography is more par for the course.