Recently there has been an exciting development published in the American Naturalist: Felsenstein has extended his method so that one can now calculate contrasts both within and among species (the conceptual figure here is taken from this paper, Felsenstein 2008). This effectively accounts for error in the estimation of species means, which can cause bias in most applications of contrasts. But there's more to this paper than measurement error, and Felsenstein waits until the end of the paper to get into what is (to me) the best bit: this new method effectively uses contrasts to link micro- and macroevolution, unifying patterns within and among species. Sound familiar? I think this is the comparative method's version of the BEST approach.
Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am. Nat. 171:713-725.