Imagine having a similar tool for phylogenetics, where people could add annotations (such as "wings developed here", "oldest fossil found at this site", "pollination mode changed here", "change in base composition took place here", etc.). A bit like MacClade on steroids, or a community driven version of the TaxonTree tool developed by the University of Maryland's Human-Computer Interaction Lab (see their page on Biodiversity Informatics Visualization).
Leaving aside the issue of file format, we'd need a way of unambiguously locating a point on a tree. An obvious solution is to use least common ancestors (same concept as most recent common ancestors), as used in phylogenetic nomenclature (although not in apomorphy-based definitions, which strike me as a disaster waiting to happen).
It's in this sort of context that I think phylogenetic names show great promise. For some nice examples of using LCA's to identify nodes, take a look at the mor server (seemingly down at present, but described in a paper by David Hibbett and colleagues doi:10.1080/10635150590947104), and Michael Sanderson's program r8s. The mor package uses phylogenetic definitions of names to locate the corresponding groups in a large phylogenetic tree, and r8s has the MRCA command to attach age constraints to nodes in a tree.
