SPOILERS:
Thor was actually dead during Civil War.
The Thor lookalike in 'Civil War' was an android, coated in cloned tissue derived from one of Thor's hairs (So sort of a 'Thorminator'), which Tony Stark had obtained way back when the Avengers were just starting up and he wanted to ascertain whether Thor was a superhuman, an alien, a mutant or actually something which could not be quantified - like a god. What surprises me most about all of this is that Thor even has DNA. The Thor clone - usually known as 'Clor' - had an artificial brain, so he was not human in any sense of the word; nobody is entirely sure who programmed him, but there is strong evidence it was Henry Pym; the Thor clone was apparently a group project by Tony Stark, Reed Richards and Henry Pym. The problem with that was that, at the time, Henry Pym was actually Criti-Noll, a Skrull infiltrator.
Anyway, Clor kept repairing himself after the moment above and, after discovering he really was just a copy of Thor, changed his name to Ragnarok and fought the original, only to be defeated again. Eventually he was inured into the Thunderbolts, and the evil dr.June Covington (aka 'Toxic Doxie') used the advanced technology of an alternate universe they travelled to to restore him completely, without his artificial brain. So then he technically really was a clone of Thor, albeit retaining his 'Clor / Ragnarok' memories; he finalized the deal by seizing the hammer of the alternate universe Thor to see whether he was worthy, or just a carbon copy. Then this happened...
Whatever he is now, he seems more heroic than anything, but his current whereabouts are unknown.