I also have the Autodesk Maya 2009: Foundation and am working through it at the moment.
I wouldn't necessarily call it a reference as it seems to be mostly a project-based tutorial/introduction to the various aspects of maya. It seems to be pretty good and I'm learning lots, but I'm excited to move past that onto bigger and better things

I also have the visual quickstart guide to Maya 6, which, although I haven't used it much, seems to be more of a reference type book as it goes through how to use each of the tools and things individually. I know it's a bit dated, but I figure most of the tools will still be relevant for 99% of what will be used (especially by a beginner like me).

Just my two bits (or two cents... which, now that I think about it, doesn't compare at all...)