A solution with two bonuses:
First lets define :
$$X=\int_0^1\frac{\ln^2(1+x)}{1+x^2}dx$$
$$Y=\int_0^1\frac{\ln(1-x)\ln(1+x)}{1+x^2}dx$$
$$Z=\int_0^1\frac{\ln x\ln(1+x)}{1+x^2}dx$$
also we will be using the two auxiliary integrals (proved below):
$$\mathcal{J}=\int_0^1\frac{\ln^2(1-x)}{1+x^2}dx=-2\ \text{Im}\operatorname{Li}_3(1+i)+\frac{3\pi}{16}\ln^22+\frac{7}{64}\pi^3$$
$$\mathcal{K}=\int_0^\infty\frac{\ln^2(1+x)}{1+x^2}dx=2\ \text{Im}\operatorname{Li}_3(1+i)$$
My technique here is to establish three relations and solve them as a system of equations.
First relation:
We know that the value of $\int_0^1\frac{\ln^2 x}{1+x^2}dx=\frac{\pi^3}{16}$ and by subbing $x\mapsto \frac{1-x}{1+x}$ we get
$$\frac{\pi^3}{16}=\int_0^1\frac{\ln^2(1-x)}{1+x^2}dx-2\int_0^1\frac{\ln(1-x)\ln(1+x)}{1+x^2}dx+\int_0^1\frac{\ln^2(1+x)}{1+x^2}dx$$
substitute the value of $\mathcal{J}$ to get
$$X-2Y=2\ \text{Im}\operatorname{Li}_3(1+i)-\frac{3\pi^3}{64}-\frac{3\pi}{16}\ln^22\tag1$$
Second relation:
We start with $\int_0^1\frac{\ln x\ln(1-x)}{1+x^2}dx$ where if we sub $x\mapsto \frac{1-x}{1+x}$ we get
$$\int_0^1\frac{\ln^2(1+x)}{1+x^2}-\int_0^1\frac{\ln(1-x)\ln(1+x)}{1+x^2}-\int_0^1\frac{\ln x\ln(1+x)}{1+x^2}=-\ln2\underbrace{\int_0^1\frac{\ln\left(\frac{1-x}{1+x}\right)}{1+x^2}}_{x\mapsto (1-x)/(1+x)}$$
or
$$X-Y-Z=\ln2\ G\tag2$$
Third relation:
We manipulate the integral $A$:
$$\int_0^1\frac{\ln^2(1+x)}{1+x^2}dx=\int_0^\infty\frac{\ln^2(1+x)}{1+x^2}dx-\underbrace{\int_1^\infty\frac{\ln^2(1+x)}{1+x^2}dx}_{x\mapsto 1/x}$$
$$=\int_0^\infty\frac{\ln^2(1+x)}{1+x^2}dx-\int_0^1\frac{\ln^2(1+x)}{1+x^2}dx+2\int_0^1\frac{\ln x\ln(1+x)}{1+x^2}dx-\underbrace{\int_0^1\frac{\ln^2x}{1+x^2}dx}_{\pi^3/16}$$
substitute the value of $\mathcal{K}$ we get
$$X-Z=\text{Im}\operatorname{Li}_3(1+i)-\frac{\pi^3}{32}\tag3$$
Now we solve the three equations $(1)$, $(2)$ and $(3)$:
$$X-2Y=a,\quad a=2\ \text{Im}\operatorname{Li}_3(1+i)-\frac{3\pi^3}{64}-\frac{3\pi}{16}\ln^22$$
$$X-Y-Z=b,\quad b=\ln2\ G$$
$$X-Z=c,\quad c=\text{Im}\operatorname{Li}_3(1+i)-\frac{\pi^3}{32}$$
we get
$$X=a-2b+2c=4\ \text{Im}\operatorname{Li}_3(1+i)-\frac{7\pi^3}{64}-\frac{3\pi}{16}\ln^22-2\ln2\ G$$
$$Y=-b+c=\text{Im}\operatorname{Li}_3(1+i)-\frac{\pi^3}{32}-\ln2\ G$$
$$Z=a-2b+c=3\ \text{Im}\operatorname{Li}_3(1+i)-\frac{5\pi^3}{64}-\frac{3\pi}{16}\ln^22-2\ln2\ G$$
Proof of $\mathcal{J}$:
Note that $\frac1{1+x^2}=\text{Im}\frac{i}{1-ix}$ and by using the identity
$$\int_0^1\frac{y\ln^{n}(x)}{1-y+yx}dx=(-1)^{n-1}n!\operatorname{Li}_{n+1}\left(\frac{y}{y-1}\right)$$ which can be found in the book Almost Impossible Integrals, Sums and Series page 5, we get
$$\mathcal{J}=\int_0^1\frac{\ln^2(1-x)}{1+x^2}dx=\text{Im}\int_0^1\frac{i\ln^2(1-x)}{1-ix}dx, \quad x\mapsto 1-x$$
$$=\text{Im}\int_0^1\frac{i\ln^2(x)}{1-i+ix}dx=-2\ \text{Im}\operatorname{Li}_{3}\left(\frac{i}{i-1}\right)=\boxed{\frac{3\pi}{16}\ln^22+\frac{7}{64}\pi^3-2\ \text{Im}\operatorname{Li}_3(1+i)}$$
where the last result follows from using the trilogarithm identity
$$\small{\operatorname{Li}_3(x)+\operatorname{Li}_3(1-x)+\operatorname{Li}_3\left(\frac{x}{x-1}\right)=\frac16\ln^3(1-x)-\frac12\ln x\ln^2(1-x)+\zeta(2)\ln(1-x)+\zeta(3)}$$
Proof of $\mathcal{K}$:
This integral was nicely calculated by Cornel:
$$\int_0^\infty\frac{\ln^2(1+x)}{1+x^2}dx\overset{x\mapsto 1/x}{=}\int_0^\infty\frac{\ln\left(\frac{x}{1+x}\right)}{1+x^2}dx\overset{x/(1+x)\mapsto x}{=}\int_0^1\frac{\ln^2x}{x^2+(1-x)^2}dx$$
$$=\text{Im} \int_0^1\frac{(1+i)\ln^2x}{1-(1+i)x}dx=\boxed{2\ \text{Im} \operatorname{Li}_3(1+i)}$$
where the last result follows from using the identity
$$\int_0^1\frac{y\ln^nx}{1-yx}dx=(-1)^{n-1}n!\operatorname{Li}_{n+1}(y)$$
which can be found in the same book mentioned above same page.
Addendum:
If we follow the same approach of evaluating $\mathcal{J}$ and $\mathcal{K}$ we can get the two generalizations:
$$\int_0^1\frac{\ln^n(1-x)}{1+x^2}dx=(-1)^{n-1}n!\ \text{Im}\left\{\operatorname{Li}_{n+1}\left(\frac{i}{i-1}\right)\right\}$$
$$\int_0^\infty\frac{\ln^n(1+x)}{1+x^2}dx=(-1)^nn!\ \text{Im}\{\operatorname{Li}_{n+1}(1+i)\}$$