Having said that, not all paraphyletic groups survived the changeover: Protozoa, Apterygota, Labyrinthodontia, Proteutheria, Thecodontia (though somebody once tried), Condylarthra, etc. But these tended to be used as wastebasket groups, so they're probably best left behind.
In a frankly overzealous effort to avoid coining any few names, Laurin & Reisz (1995 onwards) gave phylogenetic definitions to Eosuchia (diapsids except araeoscelidians, sort of), Stegocephalia (contains all vertebrates known to have limbs -- I forgot what the definition is, but it's not apomorphy-based), and Labyrinthodontia (similar to Stegocephalia, but a bit bigger or smaller). Michel actually uses Stegocephalia in this sense, but I think nobody else does, and (though perhaps only due to lack of occasions) even he hasn't used Labyrinthodontia.
Ancient meanings: Eosuchia = the diapsid rhizome group, compare Thecodontia, the archosaurian rhizome group; Stegocephali/-a/-ia = limbed vertebrates other than lissamphibians and amniotes; Labyrinthodontia = roughly the big stegocephalians, means, all except the lepospondyls.