I've been through this aprt of the game like 5-6 times now, easy. And this is like the third time I've taken this path, where I side with "myself" or "yes man". And I went over to kill mr.house right after talking to him after offing benny for the chip, well after i got back from mr house's, yes man is gone. I waited 8 hours and no dice. He simply vanished. I looked at my quests and it says that im supposed to return to him, so thats not the problem. I also went back to mr houses to see if yes man was already uploaded. Like I said, third time on this path, never did anything odd at all. Right over to house, dead, come back, gone. WTH?

I haven't been through this part yet, but after I talked to Yes Man, I randomly found him hanging out in front of one of the other casinos in New Vegas... At least, it was ONE of the buildings in New Vegas. I would have never distinguished him from the other Securitrons in the area, were it not for his happy face and the fact that I noticed his name when I passed my cross-hair over him for a second.

I hope this helps a bit.