I've begun to notice something in Fallout 3 about the Karma and its sort of causing me to chuckle a bit.

Example I came across Gildershade and the nuka-cola girl. She asked me to find her quantum which is no big deal. I had since starting this character, collected 27 bottles worth without even stopping into the nuka-cola factory. Apparently though giving the quantum to the man who wants in her pants, despite her naive "he won't fit" response... is negative karma.

However promising to have a threeway with him if he brings you quantum for her (black widow perk) which sends him off to his death in the factory gets you good karma when you give her the bottles.

That doesn't make sense to me.

Then there is the whole vault incident when you rescue your dad from the simulation. Killing the residents which simply lets the overseer reset the simulation is terrible negative karma. But killing them outright by using the machine to actually kill everyone for real is good karma.

I think the system needs some work.

That part makes sense to me, you're ending their misery. They've been trapped in this non-existence, and tortured by Von Braun, for over 200 years. You're finally giving them some rest. It seems pretty obvious that after 200 years in a pod their actual bodies won't last long if you simply set them free, so you're giving them a quick death instead of dragging it out.