I have managed to solve it in one way, but I became very interested in this failed attempt.
$$ \int_0^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x = \int_0^\infty \frac{\ln(x)}{(1+x^2)^2} {\rm d}x - \int_0^\infty \frac{\ln(x)}{(1+x^2)^3} {\rm d}x $$
We only have to show that those two on the right are equal. And numerical evaluations seem to suggest that they both are in fact $-\frac{\pi}{4}$ but I don't know how to break these down.
I am currently really interested in proving this $$ \int_0^\infty \frac{\ln(x)}{(1+x^2)^2} {\rm d}x = \int_0^\infty \frac{\ln(x)}{(1+x^2)^3} {\rm d}x = -\frac{\pi}{4} $$
Anyway, here's my trivial solution using $u = \frac1x$:
$$ \begin{align} \int_0^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x & = \int_0^1 \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x + \int_1^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x \\ & = \int_\infty^1 \frac{\frac{1}{u^2} \ln(\frac1u)}{(1+\frac{1}{u^2})^3} \frac{-1}{u^2} {\rm d}u + \int_1^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x \\ & = -\int_1^\infty \frac{\ln(u)}{u(u+\frac{1}{u})^3} {\rm d}u + \int_1^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x \\ & = - \int_1^\infty \frac{u^2 \ln(u)}{(1+u^2)^3} {\rm d}u + \int_1^\infty \frac{x^2 \ln(x)}{(1+x^2)^3} {\rm d}x \\ & = 0 \end{align} $$
I'm sure there are many more interesting methods for cracking this integral, since it's so closely related to the popular $\int_0^\infty \frac{\ln(x)}{1+x^2} {\rm d}x = 0$. Please share them if you do come up with any.