Law-- rather than physical possibility-- regulated the number of times a Time Lord could regenerate. After 12 regenerations, the Rassilonic force took the Time Lord's essence and bio data into a matrix. (Deadly Assassin, Shada)
Time Lords were able to extend the allotted number of regenerations when the need existed. For example, in The Five Doctors, the master is told that if he helps the High Council he will be given a "new regeneration cycle" which implies he will be allowed or given 12 more regeneration before being sucked into the Matrix. In the New Series, the Master claims he was given new regenerations but in the end chooses not to use them. (The Sound of Drums)
Another demonstration that the matrix�s power was regulated rather than forced is that, at the end of the Master's regeneration cycles, he transfers his essence into a new body and lives. If the 12 regenerations were a physical limit, his essence would have been dead or powerless to act and survive the change. (The Keeper of Traken)
Therefore, if Gallefrey, Rassilon, and the power behind the matrix has ceased to exist, the Doctor�s essence will not be taken from him after 12 regenerations. His essence will not be changed and he will still retain the ability to regenerate, possibly as many times as he likes.
In Mawdryn Undead the Doctor still has the limit of 12 regeneration by the Rassilonic law. However, I think the important detail to recognized in this episode is that regeneration energy can be transferred, or even possibly renewed. It is also good to note that the TARDIS herself can transfer the same type energy as used for regeneration. One could theorize here that the Doctor could draw energy from the TARDIS to regenerate when he himself is too weak. It is possibly he did this in Journey�s End, thereby causing the TARDIS to be temporarily destroyed.
Although the Doctor is known to bluff, he often did tell others that he had more regeneration than 12 -- usually some very high number. In Creature from the Pit, he claims he has regenerated many more times than 12 already.