Right now there are some very valid questions being asked about how treelike we might expect to find the history of prokaryotes. Conflicting phylogenetic trees derived from homologs-that-look-like-orthologs are probably in large part due to horizontal (or lateral if you prefer) gene transfer. Some might be due to hidden paralogy, poor phylogenetic models and maybe some other things, but for the most part, if we are careful about making trees, we find that the best explanation is horizontal gene transfer.
So, has this completely destroyed the phylogenetic signal for prokaryotes? I think that on the whole the answer is yes, but are there places where we might expect treelikeness to be stronger than the confusing signal? I think that the answer to this is yes!
We carried out a study in 2004 where we make a phylogenetic supertree from input trees that were derived from single-copy genes (these have the best chance of being true orthologs). When we compared the input trees to the over-arching supertree, we found that, depending on the data we were looking at, we saw either a complete mess or we saw some order.
The complete mess was the data that came from a bunch of genomes that were from really, really diverse prokaryotes.
The reasonable compatibility came from genomes that were clearly more closely-related on average.
Now, we didn't lok at really really closely related genomes (though we have elsewhere), but we know that, say, within the genus Neisseria, there is very little agreement between gene trees.
Therefore, we concluded eight years ago that a tree-like phylogeny only existed near to the tips of the prokaryotic phylogenetic history.
I'm surprised that more studies of this nature haven't been carried out, though some have. I don't think the answer will change though.
There is loads of disagreement between phylogenetic trees in prokaryotes and there is loads of agreement and one single answer to this question is not forthcoming.
In any case, why should we expect one single answer? Its biology, after all.
Creevey, C.J., Fitzpatrick, D.A., Philip, G.K., Kinsella, R.J., O’Connell, M.J., Pentony, M.M., Travers, S.A.A., Wilkinson, M., and McInerney, J.O. (2004). Does a Tree-like Phylogeny Only Exist at the Tips in the Prokaryotes? Proceedings of The Royal Society of London, Biology Series271(1557):2551-8. [pdf]