I just checked the current git HEAD of nautilus, with:
grep -RC 5 g_get_home *

I couldnt find any indication that nautilus saves the thumbnails in ~/ as a dotfile.

Could you provide the name of the particullar dotfile you are reporting?

P.S. never the less I saw that there are still a lot of references to ~/.gnome2 I wonder what that has got to do in a gnome3 application.

-> gnome-desktop

It's gnome-desktop that create those thumbnails, and stores it in ~/.thumbnails.

Created attachment 185005 [details] [review]
Use XDG cache dir for thumbnails

Created attachment 185006 [details] [review]
Use XDG cache dir for thumbnails

Created attachment 185007 [details] [review]
Use XDG cache dir for thumbnails

Created attachment 185008 [details] [review]
Use XDG cache dir for thumbnails

Need to fix it in the thumbnail spec:
http://people.freedesktop.org/~vuntz/thumbnail-spec-cache/directory.html
http://jens.triq.net/thumbnail-spec/index.html

*** Bug 523174 has been marked as a duplicate of this bug. ***

*** Bug 670112 has been marked as a duplicate of this bug. ***

*** Bug 674019 has been marked as a duplicate of this bug. ***

*** Bug 675169 has been marked as a duplicate of this bug. ***

Created attachment 213404 [details] [review]
Move thumbnails into XDG_CACHE_HOME

Created attachment 213405 [details] [review]
thumbnail: Modify to follow the XDG Basedir Spec

Review of attachment 213404 [details] [review]:

Looks good to me, fwiw

Review of attachment 213405 [details] [review]:

looks good, but we should get the spec on fd.o and refer to that as the canonical version.

*** Bug 675583 has been marked as a duplicate of this bug. ***

(In reply to comment #15)
> Review of attachment 213405 [details] [review]:
> 
> looks good, but we should get the spec on fd.o and refer to that as the
> canonical version.

Bug filed here: https://bugs.freedesktop.org/show_bug.cgi?id=49607

The thumbnail spec change has been pushed last week, so we should go ahead with this