I wonder why House would bother creating software that would only be used in the event of a system takeover, and his death.
House probably ran a program that predicted, to 95% certainty, that his "protege" (Benny/Courier) would stab him in the back and use his own network against him. Therefore he uploaded himself into a program that would be "accidently" found by any machine attempting to take over his network on his death.
I think Yes Man just becomes independent, just like Vegas. Yes Man controls the strip, the securitrons, probably following Mr House's plans, which is why the courier isn't in charge at the end.
However, since Yesman IS now able to access the complete House/Robco/Repconn network, I'm sure there are more secrets waiting: another cache of securitrons, vaults with arms etc.