In a previous life as an “archaeal genome biologist”, I spent a lot of time explaining to people why Archaea are distinct from Bacteria and Eukarya. One day, I happened across a long, detailed review paper entitled: The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. It briefly sowed seeds of doubt in my mind as to how distinct Archaea really are, until I realised that much of the analysis centred on cell membrane structure – which in my humble opinion, is not very sensible.
I’m not a phylogeneticist, nor am I wedded to any one classification scheme, but I think there are good arguments for the current three domain system. Others disagree; if that excites you, go read the discussion at evolgen and keep an eye on Sandwalk, Larry Moran’s new blog.