A closed form indeed exists for this integral:
$$\int_0^\infty\frac{\log\left(1+\frac{\pi^2}{4\,x}\right)}{e^{\sqrt{x}}-1}\mathrm dx=\pi^2\left(\log\frac{\pi\,A^9\sqrt{2}}{\Gamma(\frac{1}{4})^2}-\frac{9}{8}\right)+2\,\pi\,C,$$
where $A$ is the Glaisher-Kinkelin constant and $C$ is the Catalan constant.
A more general result:
$$\int_0^\infty\frac{\log\left(1+\frac{a}{x}\right)}{e^{\sqrt{x}}-1}\mathrm dx=8\,\pi^2\psi^{(-2)}\left(\frac{\sqrt{a}}{2\pi}\right)-\frac{a}2\left(1+\log\frac{4\pi^2}{a}\right)-2\pi\sqrt{a}\left(1+2\log\Gamma\left(\frac{\sqrt{a}}{2\pi}\right)\right),$$
where $\psi^{(-2)}(z)$ is the generalized polygamma function.
The proof is based on Binet's second formula, but I still need to sort out some details.
We make use of the identity
$$ \sum_{n=-\infty}^{\infty} \frac{1}{a^{2} - (x + n\pi)^{2}} = \frac{\cot(x+a) - \cot(x-a)}{2a}, \quad a > 0 \text{ and } x \in \Bbb{R}. $$
Then for $\alpha, \beta > 0$ it follows that
\begin{align*}
I := \mathrm{PV}\int_{0}^{\infty} \frac{\log\cos^{2}(\alpha x)}{\beta^{2} - x^{2}}
&= \frac{1}{2} \mathrm{PV} \int_{-\infty}^{\infty} \frac{\log\cos^{2}(\alpha x)}{\beta^{2} - x^{2}} \, dx \\
&= \frac{\alpha}{2} \mathrm{PV} \int_{-\infty}^{\infty} \frac{\log\cos^{2}x}{(\alpha\beta)^{2} - x^{2}} \, dx \\
&= \frac{\alpha}{2} \sum_{n=-\infty}^{\infty} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \frac{\log\cos^{2}x}{(\alpha\beta)^{2} - (x+n\pi)^{2}} \, dx \\
&= \frac{\alpha}{2} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \left( \sum_{n=-\infty}^{\infty} \frac{1}{(\alpha\beta)^{2} - (x+n\pi)^{2}} \right) \log\cos^{2}x \, dx \\
&= \frac{1}{4\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\cos^{2}x \, dx,
\end{align*}
where interchanging the order of integration and summation is justified by Tonelli's theorem applied to the summation over large indices $n$. Then
\begin{align*}
I
&= \frac{1}{4\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\cos^{2}x \, dx \\
&= \frac{1}{2\beta} \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} (\cot(x+\alpha\beta) - \cot(x-\alpha\beta)) \log\left|2\cos x\right| \, dx \tag{1}
\end{align*}
Here, we exploited the following identity to derive (1).
$$ \mathrm{PV} \int_{-\frac{\pi}{2}}^{\frac{\pi}{2}} \cot(x+a) \, dx = 0 \quad \forall a \in \Bbb{R}. $$
Now with the substitution $z = e^{2ix}$ and $\omega = e^{2i\alpha\beta}$, it follows that
\begin{align*}
I
&= \frac{1}{2\beta} \Re \mathrm{PV} \int_{|z|=1} \left( \frac{\bar{\omega}}{z - \bar{\omega}} - \frac{\omega}{z - \omega} \right) \log(1 + z) \, \frac{dz}{z}. \tag{2}
\end{align*}
Now consider the following unit circular contour $C$ with two $\epsilon$-indents $\gamma_{\omega,\epsilon}$ and $\gamma_{\bar{\omega},\epsilon}$.
Then the integrand of (2)
$$ f(z) = \left( \frac{\bar{\omega}}{z - \bar{\omega}} - \frac{\omega}{z - \omega} \right) \frac{\log(1 + z)}{z} $$
is holomorphic inside $C$ (since the only possible singularity at $z = 0$ is removable) and has only logarithmic singularity at $z = -1$. So we have
$$ \oint_{C} f(z) \, dz = 0. $$
This shows that
\begin{align*}
I
&= \frac{1}{2\beta} \Re \lim_{\epsilon \downarrow 0} \left( \int_{-\gamma_{\omega,\epsilon}} f(z) \, dz + \int_{-\gamma_{\bar{\omega},\epsilon}} f(z) \, dz \right) \\
&= \frac{1}{2\beta} \Re \left( \pi i \mathrm{Res}_{z=\omega} f(z) + \pi i \mathrm{Res}_{z=\bar{\omega}} f(z) \right) \\
&= \frac{1}{2\beta} \Re \left( - \pi i \log(1 + \omega) + \pi i \log(1 + \bar{\omega}) \right) \\
&= \frac{\pi}{\beta} \arg(1 + \omega)
= \frac{\pi}{\beta} \arctan(\tan (\alpha \beta)).
\end{align*}
In particular, if $\alpha\beta < \frac{\pi}{2}$ then we have
$$ I = \pi \alpha. $$
But due to the periodicity of $\arg$ function, this function draws a scaled saw-tooth function for $\alpha > 0$. Of course, $I$ is an even function of both $\alpha$ and $\beta$, so the final result is obtained by even extension of this saw-tooth function.
Best Answer
\begin{align} &\int_0^{\infty} \frac{\log(t+1)}{t^2+a^2} \ dt\\ =& \int_0^{\infty}\int_0^1 \frac{t}{(t^2+a^2)(1+yt)}dy \ dt\\ =& \int_0^1 \frac1{1+a^2y^2}\int_0^\infty\left(\frac{a^2y}{t^2+a^2}+ \frac{t}{t^2+a^2}-\frac{y}{1+yt}\right)dt\ dy\\ = & \ \frac\pi2 \int_0^1 \frac{ay}{1+a^2y^2}dy-\int_0^1 \frac{\ln (a)}{1+a^2y^2}\ dy- \int_0^1 \frac{\ln (y)}{1+a^2y^2}\ dy\\ =& \ \frac\pi{4a}\ln(1+a^2)-\frac1a\ln (a)\tan^{-1}(a) -\frac i{2a}(\mathrm{Li}_2(ia)-\mathrm{Li}_2(-ia)) \end{align}