Let us consider the following contour.
Fix $R>0$ a radius which is a ("big") multiple of $2\pi$, $R=R(n)=2\pi n$.
Consider the closed contour $C=C(R)$ build from the two pieces
- the segment (interval) $I=I(R)$ from $-R$ to $R$,
- the halfcircle $H=H(R)$ from $R$ to $-R$ parametrized by $t\to Re^{it}$, $t\in[0,\pi]$.
A picture would be:
$1+e^x$ in the denominator">
and the unit is $\pi$. Then we have for the given meromorphic function $f(z)= (e^z+1)^{-1}(z^2+\pi^2)^{-1}$
$$
\begin{aligned}
\int_{\Bbb R}f(x)\; dx
&
=
\lim_{n\to\infty}
\int_{-R(n)}^{+R(n)}
f(z)\; dz
=
\lim_{n\to\infty}
\int_{I(R(n))}
f(z)\; dz
\ ,
\\
0&=
\lim_{n\to\infty}
\int_{C(R(n))}
f(z)\; dz
\\
\int_{I(R)}
f(z)\; dz
+
\int_{H(R)}
f(z)\; dz
&=
2\pi i\sum_{a\text{ pole inside }C(R)}
\operatorname{Residue}_{z=a}f(z)
\ .
\end{aligned}
$$
The zero limit, when integrating on $C(R(n))$, $n\to\infty$ can be motivated as follows. The contour integral is a closed set, not passing through the poles. There is a minimal distance $\pi$ to the poles, which helps us to bound from below $|1+e^z|$, so from above $1/|1+e^z|$. Then the term $1/(x^2+\pi^2)$ is in $O(R^{-2})$, the contour length $(\pi R)$ in $O(R)$, so we land in $O(1)\cdot O(R^{-2})\cdot O(R^1)=O(R^{-1})$.
It remains to consider the sums of the residues of the poles in the upper half plane. We get:
$$
\begin{aligned}
\operatorname{Residue}_{z=i\pi}f(z)
&=
\operatorname{Residue}_{h=0\\z=i\pi+h}
\frac 1{1+e^{i\pi}e^h}\cdot
\frac 1{h+i\pi+i\pi}\cdot
\frac 1{h+i\pi-i\pi}
\\
&=
\operatorname{($h^0$-Coefficient)}_{h=0}
\frac 1{1-e^h}\cdot
\frac 1{h+2\pi i}
\\
&=
\operatorname{($h^0$-Coefficient)}_{h=0}
\frac 1{-h-\frac 12h^2+O(h^3)}\cdot
\frac 1{2\pi i}\cdot
\frac 1{1-(-h/(2\pi i))}
\\
&=
\operatorname{($h^0$-Coefficient)}_{h=0}
-\frac 1h
\left(1-\frac 12h+O(h^2)\right)
\frac 1{2\pi i}\cdot
\left(1-\frac h{2\pi i}+O(h^2)\right)
\\
&=
\operatorname{($h^0$-Coefficient)}_{h=0}
-\frac 1{2\pi i}\cdot
\frac 1h
\left(1-\frac 12h-\frac h{2\pi i}+O(h^2)\right)
\\
&=
\frac 1{2\pi i}\cdot
\left(\frac 12+\frac 1{2\pi i}\right)
\end{aligned}
$$
I really wanted to do this with bare hands, and use computer only for the check:
sage: var('z');
sage: f(z) = 1 / (1+exp(z)) / (z^2+pi^2)
sage: f(z).residue( z==i*pi )
-1/4*I/pi - 1/4/pi^2
sage: bool( f(z).residue( z==i*pi ) == 1/(2*pi*i) * (1/2 + 1/(2*pi*i)) )
True
It turns out, that all other residues (at poles in the upper half plane) are real. This time we let the computer give us some values:
sage: f.residue( z==3*pi*i )
z |--> 1/8/pi^2
sage: f.residue( z==5*pi*i )
z |--> 1/24/pi^2
sage: f.residue( z==7*pi*i )
z |--> 1/48/pi^2
sage: f.residue( z==9*pi*i )
z |--> 1/80/pi^2
sage: f.residue( z==11*pi*i )
z |--> 1/120/pi^2
and so on as in the OP, the denominators in the rational numbers appearing above (and touching $1/\pi^{2}$) are squares of odd integers, taken minus one.
Our integral is real, so we can forget all these values, getting thus:
$$
\int_{\Bbb R}
\frac{dx}{(1+e^x)(x^2+\pi^2)}
=
2\pi i \left[
\frac 1{2\pi i}
\left(
\color{blue}{\frac 12}+\frac 1{2\pi i}\right)
+
\text{real number(s)}\right]
\ ,
$$
and only the blue term survives to give us the "real answer".
Note: I was spending a lot of time trying to check / validate somehow this value numerically. This is the best i could get in pari/gp:
? \p 1000
realprecision = 1001 significant digits (1000 digits displayed)
? intnum( x=-200, +100, 1 / (1+exp(x)) / (x^2+Pi^2) )
%19 = 0.49500041117264675924354715963413516...
(And we can tacitly control the piece from $[-\infty, -200)$ using $1/(x^2+\pi^2)$.)