Just for the record, I was responding to the posters asking about the "message list", not the "mailbox list" that is in the sidebar (obviously).
The sidebar "font size" setting works for me in controlling the _size_ of the font in the sidebar. Like others, I have not found anything to control the actual font type in the sidebar.
When I deselect "use classic layout", and thus go into three columnn mode, I loose control of the message list font: it does not obey the settings.
You've defined it just right, GreenAsJade, and Mail 6.0 is unworkable until this gets fixed. It's back to the Gmail web interface for me. Very disappointing. Mail in the old view is an old-fashioned, clunky program that doesn't deal at all well with conversation threads. The new three-column view fixes that and makes a really nice program, the mail list is unreadable and the preferences don't work. Forget "think different." Just think, Apple.