Any recommendations for very flexible themes which offer secondary custom menus, a variety of sub-page layouts, and built in SEO?
What themes has your college/university used, liked, disliked?
Thematic is hugely flexible -- css classes for everything, many widget areas, lots of hooks to customize, and an active forum with many solutions available. The developer is now Automattic's head theme honcho. In order to do a lot, it requires the ability to use PHP snippets. For simpler customizations, I've heard Thesis is good.
BTW, the HTML 5 version of Sandbox is Toolbox, also by Ian Stewart.