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Megaton turns hostile (lay low for a while and they'll become friendly again). And your get negative karma. Also I think if you seduce Mr. Burke (if you're a female character with Black Widow) you don't get his love letters. Oh, and Nova retires a prostitute, so no more waking up to her next to you when you rent a room. I think that's it.
I made it into a mission like I did with Alessia Caro in Oblivion. I managed to kill him without anyone shooting at me, all you need is the dart gun, chinese stealth suit/stealth boy, and a nice perch. Watch his schedule and wait for him to exit the bar, I think you can figure out the rest.
Megaton will stop being hostile after 3 days, but there is a chance Gob can disappear from the game if you kill Moriarty (Gob is supposed to take over the saloon after killing him). You can bring Gob back through codes but he won't take over the saloon for some reason, so what I would do is make a backup save and keep killing Moriarty until Gob stops disappearing.
What kydos said. Actually usually I just shoot him in the back room with the door closed, some people turn hostile for a few seconds but if I stay hidden they go back to normal. Also I love how when you kill Moriarty the sign on the saloon changes to "Gobs Saloon".