We made our own choices in this game and when I learned of this, I knew I couldn't go YesMan. He has his own agenda, doesn't he? He uses the Courier to get where he wants to be and then will reprogram himself. He didn't mention that when he recruited the Courier.
I've seen Terminator...so, no way, YesMan.
Yes Man doesn't really have an agenda, he's too short sighted for that, and that makes him dangerous. On the other hand, anyone cooperating with Yes Man is a kindred spirit. And don't forget you use Yes Man as well, basically you are replacing Benny. But in general you shouldn't trust anyone who claims that he can't lie.
In the long run House may be the best choice for humanity (aka the greater good), an immortal autocrat that leaves his subjects alone as long as they behave themselves is preferable over both, the proto-fascist colonialists and the anachronistic club-law society. But how much does Mr. House really differentiate from the Master?
Anyway, the question of good vs. evil shouldn't really be defined by future possibilities. Otherwise we'd get into a Minority Report situation, where someone could kill a baby and claim the infant was bound to become the next Hitler.
More often than not the good side needs sacrifices, the evil side is just more open about that, and not so picky about whom to sacrifice. Roleplaying also means letting you decide whether you want to play a hero, who would sacrifice himself to get a water purifier running and fulfil his late dad's dream, or if you play a normal person mainly interested in himself and those close to him.