I brought this up back in February regarding the new stegosaur Miragaia longicollum; about how regardless of the claims made by journals, unless the guidelines put forth by the International Committee of Zoological Nomenclature (ICZN) regarding publication are adhered to (i.e., hard copy placed in at least five libraries that are explicitly identified in the document) published names in online only publications are simply not valid. Now a similar case is coming under heavy discussion.
The newly described primate Darwinius masillae (Franzen et al., 2009) has been receiving tons of press heralded as being a 'missing link' in primate evolution (however see this article in Laelaps), however, it is not only the phylogentic position and its interpretation that is being hotly debated. Now the validity of the taxonomic name is being called into question because the name was published in the online-only journal PLoS One. Carl Zimmer's blog The Loom has a great discussion of this. Check it out.
Hopefully the ICZN will soon amend the code as advocated by Harris (2004) to deal with the increasing trend of online only journals and the early online releases (ahead of print versions) now popular with many journals.
This is becoming a serious problem.
Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723
Harris, J.D. 2004. 'Published Works' in the electronic age: recommended amendments to Articles 8 and 9 of the Code. Bulletin of Zoological Nomenclature 61:138-148.