Molecular Phylogenetics and Evolution carries two articles debating the application of names to trees, which reflects tensions between two codes of nomenclatures (ICZN and Phylocode). Alain Dubois (doi:10.1016/j.ympev.2006.06.007 and
David Hillis (doi:10.1016/j.ympev.2006.08.001) present rather different views. The paper that brought things to a head is Hillis and Wilcox (2005) "Phylogeny of the New World true frogs (Rana)" (doi:10.1016/j.ympev.2004.10.007, TreeBASE S1186). I've not had time to digest this (it's Friday evening, after all), but I think it's interesting to see to what extent the systems can coexist (which is what Hillis seems to argue, if only as a transitional stage), or whether they are simply incompatible.