The Dark Brotherhood, because they have been able to survive every single supposed extermination of the brotherhood for hundreds (or perhaps thousands) of years. They are resilient, cunning, and ruthless and outlasted the Morag Tong
It's pretty difficult to fully kill off something that has Sithis/Padomay as their Patron...
One of the two original beings in the multiverse... yeah, something tells me that the Dark Brotherhood will be around for quite a while. Which is fine with me as Assassin type characters are my favorite to play and the Dark Brotherhood is easily my favorite Faction! In Morrowind, all of my characters that I ever created were in the Morag Tong. In Oblivion and (now) Skyrim, it has always been the Dark Brotherhood.
With my Dunmer Assassin leading the Dark Brotherhood as the true Listener, and the Emperor's blood still fresh on my blades, how could the Dark Brotherhood not rebuild and make the public fear it all across Tamriel once again? The public in Skyrim's cities already whisper the name of the DB in fearful tones. Even the random guard greets me with a "Hail Sithis" (though I do apparently need to work on my anonymity...). Soon, all of Tamriel will once again shudder in fear at every flickering shadow.
The Dark Brotherhood will most definitely be back, though I wouldn't mind having an Elder Scrolls where most of the Assassin's don't get nuked during the Questline... that would be a nice change.
The Thalmor even have their own extermination/assassin squads, maybe have the Dark Brotherhood take offense to this as encroachment in their territory/industry and start wiping out these Thalmor Squads. Or on the flip side, that Thalmor start hiring the DB to take out those who are impeding their plans.
As long as Sithis wants Souls, there will be a Dark Brotherhood.