From http://www.illwinter.com/ :
19th November 2012 - Dominions 3 no longer sold by Shrapnel Games
Dominions 3 is no longer sold by Shrapnel Games, so it is difficult to buy right now. However we intend to sell Dominions 3 on Desura as soon as possible, hopefully December 1st.
To elaborate somewhat on that, Illwinter's contract for the distribution of Dominions 3 with Shrapnel Games expired a few days ago. Illwinter will publish the game through Desura, the target date being in the quoted section. The pricing on Desura and other such details are yet to be determined (or if they have been, Illwinter is keeping it to themselves).
Furthermore, patch 3.28 is in beta testing at the moment:
I figured there might be a bunch of people here who would find this news of interest.
Tom, it may be presumptuous of me to ask, but would this call for a sort of reprisal of Dom3 on the main page of Qt3? Perhaps after Dom3 is released on Desura?