What will you be shooting or do you like to shoot?
The D800 is different from the D3s: more pixels but more susceptible to camera movement especially at slower shutter speeds; greater dynamic range but noisier at at higher ISO; lower burst rate if you shoot action.
Those are a few points of comparison, but without knowing what you want to do, it's hard to make a recommendation.
Before i bought my D800, i did consider D3S used. The price is about the same. The reasons I choose D800 are it is lighter, more MP, new technology. I use it for landscape, people and travel. Some people prefer D3S as it has higher FPS and ISO.
I feel like my D800E has elbowed aside my D4 in many shooting situations. But I've had the D4 for 7 months and D800E only about 6 weeks, so I'm still in testing mode and the D800 is getting more work as a result.
Certainly I think the full-sized bodies are more specialized a tool and the D800-sized bodies are more generalized a tool. But yes the smaller bodies are not better in every way, for example such as extreme speed, AF, FPS, ruggedness and low light ability, so need more thoughts from you...
The D3S and D800 would complement each other in this regard but an either/or choice is rendered more difficult depending on what you need.