The worst faction for re-emergences after the Pope I would say has to be the Hungarians.
They seem to re-emerge all the time. I suspect the reason for this is that their main territory is all fairly inland. Inland provinces tend to be less loyal due to the 'number of turns to move your king to the province' factor being much higher because he can't just get there in a turn like he could if it was costal and you had a sea-link.

English rarely re-emerge I find. Possibly for the same reason.