Note that $\sqrt{(x-y)^2} = |x-y| = \begin{cases}x-y & y < x < L\\ y-x & 0<x<y\end{cases}$.
Thus, $\displaystyle\int_0^L\int_0^L \sqrt{(x-y)^2}\,dx\,dy = \int_0^L\int_0^y (y-x)\,dx\,dy + \int_0^L\int_y^L (x-y)\,dx\,dy$.
Both of these integrals are straightforward to evaluate.
EDIT: The OP just clairified that he specifically wants to use a change of variables to get the answer instead of evaluating that integral in the easiest way possible.
Let's perform the substitution $u = x-y$, $v = x+y$. Then, $x = \frac{u+v}{2}$ and $y = \frac{-u+v}{2}$.
The Jacobian is $J(u,v) = \left|\begin{matrix}\frac{\partial x}{\partial u} & \frac{\partial x}{\partial v} \\ \frac{\partial y}{\partial u} & \frac{\partial y}{\partial v}\end{matrix}\right| = \left|\begin{matrix}\frac{1}{2} & \frac{1}{2} \\ -\frac{1}{2} & \frac{1}{2}\end{matrix}\right| = \dfrac{1}{2}$.
To get the bounds, draw a picture. If $0 \le x,y \le L$, then $-L \le x-y \le L$. So, $-L \le u \le L$.
For any fixed $u > 0$, the line $x-y = u$ intersects the square $0 \le x,y \le L$ at the points $(u,0)$ and $(L,L-u)$. Hence, $u \le x+y \le 2L-u$ if $u > 0$.
For any fixed $u < 0$, the line $x-y = u$ intersects the square $0 \le x,y \le L$ at the points $(0,-u)$ and $(L+u,L)$. Hence, $-u \le x+y \le 2L+u$ if $u < 0$.
This can be consolidated into $|u| \le x+y \le 2L-|u|$. Hence $|u| \le v \le 2L-|u|$.
Therefore, the change of variables gives us: $\displaystyle\int_0^L\int_0^L \sqrt{(x-y)^2}\,dx\,dy = \dfrac{1}{2}\int_{-L}^{L}\int_{|u|}^{2L-|u|} |u|\,dv\,du$
Since the inner integrand is constant w.r.t. $v$, this becomes $\displaystyle\dfrac{1}{2}\int_{-L}^{L}(2L-2|u|)|u|\,du$.
This is a single integral which can be easily evaluated.