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I installed highlight parentheses and highlight sexps and configured them to look nice in my .emacs. As you can see, the former highlights both the current sexp you're operating in, as well as its parent sexp, so it's easier to tell where you are. The latter is what's turning on the rainbow parentheses, so it's easy to tell which parens match up to which in the code you're operating on.
To top that off, I'm now using paredit which I learned of through Emacs Rocks! This has taken a bit to get used to, but it makes operating on lisp really feel like operating on the structure of the code way more than I've ever experienced.
All fun emacs extensions!