I. $k=4n+3.\;$ From this post, one knows that $$\sum_{n=1}^\infty \frac{n^{3}}{e^{2n\pi}-1} = \frac{\Gamma\big(\tfrac{1}{4}\big)^8}{2^{10}\cdot5\,\pi^6}-\frac{1}{240}$$ and a Mathematica session reveals$$\sum_{n=1}^\infty \frac{n^{7}}{e^{2n\pi}-1} =\frac{3\,\Gamma\big(\tfrac{1}{4}\big)^{16}}{2^{17}\cdot5\,\pi^{12}}-\frac{1}{480}$$ $$\sum_{n=1}^\infty \frac{n^{11}}{e^{2n\pi}-1} =\frac{189\,\Gamma\big(\tfrac{1}{4}\big)^{24}}{2^{22}\cdot5\cdot13\,\pi^{18}}-\frac{691}{65520}$$
and so on. The $691$ is a clue that Bernoulli numbers are involved.
II. $k=4n+1.\;$ It evaluates to a rational number, $$\sum_{n=1}^\infty \frac{n^{5}}{e^{2n\pi}-1} =\frac{1}{504}$$ $$\sum_{n=1}^\infty \frac{n^{9}}{e^{2n\pi}-1} =\frac{1}{264}$$ $$\sum_{n=1}^\infty \frac{n^{13}}{e^{2n\pi}-1} =\frac{1}{24}$$
etc, with the last mentioned in this post.
Q: What are the general forms of I and II in terms of the Bernoulli numbers? (And a reference to Ramanujan's Notebooks, if possible.)
(Note: 2019 edit to 2016 post)
Since the $\Gamma(n)$/pi ratio involved has a simple form in terms of the elliptic integral singular value $K(k_n)$, turns out it was just the case $\tau=\sqrt{-1}$,
$$\beta_1=\frac{\Gamma\big(\tfrac14\big)^8}{2^8\pi^6}=\left(\frac{K(k_1)}{\pi}\right)^4$$
By analogy, the case $\tau=\sqrt{-3}$,
$$\color{red}{\beta_3}=\frac{3\Gamma\big(\tfrac13\big)^{12}}{2^9\cdot2^{1/3}\,\pi^8}=\left(\frac{K(k_3)}{\pi}\right)^4$$
So alternatively,
$$\sum_{n=1}^\infty \frac{n^{3}}{e^{2\pi\,n}-1} = \frac1{20}\beta_1-\frac{1}{240}$$
$$\sum_{n=1}^\infty \frac{n^{7}}{e^{2\pi\,n}-1} =\frac{3}{10}{\beta_1}^2-\frac{1}{480}$$
and a quick test showed,
$$\sum_{n=1}^\infty \frac{n^{3}}{e^{2\pi\sqrt3\,n}-1} = \frac{1}{16}\color{red}{\beta_3}-\frac{1}{240}$$
$$\sum_{n=1}^\infty \frac{n^{7}}{e^{2\pi\sqrt3\,n}-1} = \frac{17}{32}\color{red}{{\beta_3}^2}-\frac{1}{480}$$
and so on.