Dechonization (a blog about comparative methods)

The R for Phylogenetics Hackathon (NESCent resource on R for Phylogenetics)

Bodega Bay Phylogenetics Workshop (lectures and problem sets)

The Comparative Primatology Research Group (Charlie's lab web pages)

Time Tree (divergence times)

10kTrees (primate phylogeny)

Phylogenetic targeting (identifying species to study in the future)

PhyloDiversity (various researchers and resources)

CRAN Task View (overview of statistical packages in R)

Brian O'Meara's site (comparison of packages, other info)

R-Sig-Phylo (listserv for R-phylogenetics, worth checking out!)

The Comprehensive R Archive network