[@MrDidact] To the extent of my knowledge, the only non-lore/cannon houses that are depicted within the game appear everywhere else but Westeros. George R.R. Martin and those associated with him in crafting lore, made a pretty clear depiction of the Houses in Westeros, either in the main book line, or in subsequent anthologies. ((I.E. http://awoiaf.westeros.org/index.php/A_Song_of_Ice_and_Fire, http://awoiaf.westeros.org/index.php/A_Song_of_Ice_and_Fire_Campaign_Guide, http://awoiaf.westeros.org/index.php/The_World_of_Ice_and_Fire, and http://www.westeros.org/Citadel/Heraldry/)) 

These all paint the world of Westeros, in great detail. As for the Crusader Kings 2, A Game of Thrones mod, based all of its work off of the collected source material, and crafted detailed family trees. I will look into the family tree's of the four Houses who may have been wiped out by the start of this timeline, and get back to you. As always, its your call chief, and I shall defer to you with your final decision. ((Thus far though, I have not found any regions within the CK2 AGoT map that do not correspond with Houses in lore. Aside from Oldstones and Summerhall being ruins, all other regions are occupied at the moment, except for regions that have the same Lord presiding over them. (I.E. House Rykker in the Crownlands with rule over both Duskendale and Hollard Hall, House Tully with the Lordship over Riverrun, The Blue Fork, The Red Fork, and Branstone, and the final region I can find that is up in the air would be Moat Cailin, it in itself a ruin, with no permanent garrison or lord ruling over it. There may be other examples of one house holding de jure rule over multiple areas, but these are the ones I could find as of right meow.) 

And the reason I solely focused on the Crownlands, is that you are the main player for that region, and being GM, you could make certain decisions as to what houses may have gone silently into the long night. There could always be cousins, or intermarriage claims from other houses, but at the end of the day, you are the narrator/dungeon master for our adventure. Plus, with being of relations to the Targaryens, Aerion wants to be close to home, but with enough space to be able to breathe on his own. Sort of like the Lannister's of Lannisport (Lanny, Lannet, Lantell etc).

As for the Lannisters of Lannisport, it is still a rather large city and castle neighboring Casterly Rock. They comprise a large region just south of Casterly Rock. For all intents and purposes, they are more than a non-landed gentry, since they have the Lordship over that particular region, and give their fealty to the Higher Branch of House Lannister. Anyhow, I will wait for your final decision in the matter. 
[hider=Lannisport Region Reference][IMG]http://i63.tinypic.com/11m93eq.png[/IMG][/hider]