There are lots of different ways of arriving at the relativistic relations involving mass, energy, and momentum such as $E=mc^2$ and $m^2=E^2-p^2$ (the latter with $c=1$). One that I've seen in some textbooks is to start with the equation $W=\int F dx$ for mechanical work. Here is a particularly careful and rigorous version, which makes it explicit that this is a nontrivial assumption, along with $F=dp/dt$: http://www.physicsforums.com/showthread.php?p=2416765 Historically, Einstein made use of $W=\int F dx$ in section 10 of his 1905 paper on SR http://www.fourmilab.ch/etexts/einstein/specrel/www/ . This was before the "Does the inertia of a body..." paper, in which he derived $E=mc^2$ and gave it its full relativistic interpretation. Einstein later decided that force wasn't a very useful concept in relativity and stopped appealing to it.
What I have never seen in any of these treatments (neither the careful ones above nor the sloppy ones in some freshman physics texts) is any argument as to why the nonrelativistic relation $W=\int F dx$ should be expected a priori to hold without modification in SR. If one has already established the form and conservation of the energy-momentum four-vector, then I don't think it's particularly difficult to show that $W=\int F dx$. But what justification is there for assuming $W=\int F dx$ before any of that has been established? Is there any coherent justification for it?
(A secondary problem with some of these treatments based on $W=\int F dx$ is that they need to establish the constant of integration.)