The comics kind of toyed with the concept of the meta-crisis becoming the Valeyard, in the "Forgotten" series; however the whole thing turned out to be a bad dream caused by an alien parasite.
During the Matt Smith era, oddly enough, a very similar concept showed up in "Amy's Choice" with the Dream Lord.
Given that the Valeyard is between the twelfth and final incarnation, given how "Time of the Doctor" sort of moved that goalpost quite a bit I don't think it's something that needs to be brought up (although the Valeyard of course has been name-dropped a few times).
I personally always liked the theory that the Valeyard is, like the Watcher in Logopolis and K'anpo/Cho'Je, a sort of projection to help with particuarly nasty regenerations (Like how pretty much a lot of the Doctor's insides were probably jelly after falling from Pharos), perhaps subconsciously created by the Doctor somehow but sort of only half-existing. In the Third Doctor story "The Three Doctors", we see the Doctor grapple with Omega's "Dark side" as well, which was kind of a weird thing too (and hasn't really been followed up since).