Calixar, my take was that the unnamed villan we hear saying Silence Will Fall is the one who likely set up the Alliance, took over the Tardis while River was in it and tried to destroy the universe. His true identity is still unknown, but is still around, just thwarted for now, as acknowledged by The Doctor as he leaves in the Tardis post wedding. That will be picked up in Season Six.
The Tardis in The Lodger appears to be a mystery for now. I suppose you could write it off as an occurence for The Lodger Ep only but given Moffat's scattering of clues that resurface later, I am wondering if it is indeed a clue or a red herring. Again, you don't see many Tardises around; if an attempt to build something like one, who has that know how ? If it really was one, where is the Time Lord who once flew it or the person who stole it from the original pilot?