Boned from
Wiktionary and
Urban Dictionary. Wiktionary basically attributes it to Futurama's pilot. Urban Dictionary references Futurama. However, some of the higher entries on UD infer, in my opinion, that it has roots with "fuck", as in to bone someone ([Bender] WOOOOOOO!!! [/Bender]). Personally, I think that it 's likely been used before Futurama in select groups of people to mean both to have sex with another person and to be screwed, yet the "we're screwed" meaning, the more used meaning, didn't come to prominence until after Futurama's pilot.
Personally, I use "boned" in everyday speak, and nobody seems to think that it's obscene at all.