In 2005 Season Episode "The End of the World " - Jabe Ceth Ceth Jafe (the cute Tree-Lady) uses her scanner to ID the Doctors species, the scanner registers some disbelief and refuses to confirm he is a Time-Lord initially.
This creates a HUGE hole in New-Who's continuity.
IF the Time Lords are functionally extinct (I.E. Missing from Historical and Fossil records) which is the 'official line' - how TF does Jabes scanner have a reference to them?!?!?!?!
How do the Krillitaine or anyone else know about them for that matter, in Classic Dr Who the Time Lords were shrouded in mystery - yet nowadays it seems like everyone knows who they are/were, what they were capable of, and their Area Code!
The term "Time War" is applied to at least two types of time-spanning conflicts in the Doctor Who universe. The first type of time war is where the two sides are fighting the war across different points in history, separated by centuries or millennia - this has been seen in such stories as "The Wargames" and referenced to in "The Five Doctors".
The second type of time war is where Time itself is used as a weapon, with preemptive strikes, time-loops, temporal paradoxes, and the reversal of historical events.
Logic dictates that the "Last Great Time-War" would have used both techniques, we saw the 8th Doctors TARDIS "re-wind" Time for example in the Doctor Who TV Movie for example; illustrating such techniques SHOULD they be required.
Its all just another example of the 'fuzziness' involved in the shows 'Bible' - don't get me wrong, the individual stories/episodes are great. But all this 'confusion' makes running the RPG quite difficult.
Romana is trapped in E-Space (we have to ignore the Books as they aren't strictly canon), so technically she would still be alive too. The Meddling Monk, whatever happened to him.
All these questions (and more) need to be addressed by the Doctor Who Games Master (Time Master?) when setting up his campaign. Its going to get VERY boring for his players very quickly if one of the Players HAS to be the Doctor.
One option I personally favour is a new Gallifreyan colony made up of survivors of the Time War (much like the Vulcan colony in the new Star Trek Movie), out of desperation they would re-instate the Celestial Intervention Agency - but this time they would have a new mission objective, to ensure the survival or the Time Lord race. Rather than their original function as Spies and infitrators (It was said that they "don't even know which side they're on").
But, as with all RPG's its all horses for courses . . . .