I tried a while ago to evaluate this integral using a generalization of Ramanujan's Master Theorem referred to as the method of brackets.
(I've previously evaluated integrals using this method here and here.)
I even had brief email exchange with Dr. Karen T. Kohl about this particular integral, someone who has authored and coauthored papers on this method.
I'm going to show what happens if you use this method to evaluate the case $\nu =0$ .
Let's first assume that $a>2$.
The Bessel function of the first kind of order zero has the series representation $$J_{0}(az) = \sum_{m=0}^{\infty} \frac{(-1)^{m}}{m!} \, \frac{1}{\Gamma(m+1)} \left(\frac{a^{2}z^{2}}{4} \right)^{m}. $$
And the square of the Bessel function of the first kind of order zero has the series representation $$J_{0}(z)^{2} = {_1F_2} \left(\frac{1}{2};1,1;-z^{2} \right) = \sum_{n=0}^{\infty} \frac{
(-1)^{n}}{n!} \, \frac{\Gamma \left(n+ \frac{1}{2} \right)}{\Gamma \left(\frac{1}{2} \right)} \frac{1}{\Gamma(n+1)^{2}} \, z ^{2n}.$$
Therefore, the integral $\int_{0}^{\infty} J_{0}(ax) J_{0}(x)^{2} \, \mathrm dx $ has the corresponding bracket series $$\sum_{m=0}^{\infty} \sum_{n=0}^{\infty} \phi_{m,n} \, \left(\frac{a}{2} \right)^{2m} \frac{1}{\Gamma(m+1)} \frac{\Gamma \left(n+ \frac{1}{2} \right)}{\Gamma \left(\frac{1}{2} \right)} \frac{1}{\Gamma(n+1)^{2}} \, \langle 2m+2n+1 \rangle. $$
Since there are two indices but only one bracket, there are two cases to look at.
If we let $m$ be a free parameter, then the bracket vanishes if $n= -m- \frac{1}{2} $,
and we have the contribution $$S_{1} = \frac{1}{2} \sum_{m=0}^{\infty} \phi_{m} \left(\frac{a}{2} \right)^{2m} \frac{1}{\Gamma(m+1)} \frac{\color{red}{\Gamma(-m)}}{\Gamma \left(\frac{1}{2} \right)} \frac{1}{\Gamma\left(-m + \frac{1}{2}\right)^{2}} \, \Gamma \left(m+ \frac{1}{2} \right). $$ However, since the terms of this series are not finite, we discard it.
If we let $n$ be a free parameter, then the bracket vanishes if $m = - n - \frac{1}{2},$ and we have the contribution $$ \begin{align} S_{2} &= \frac{1}{2} \sum_{n=0}^{\infty} \phi_{n} \, \left( \frac{a}{2} \right)^{-2m-1} \frac{1}{\Gamma \left(-n+ \frac{1}{2} \right)} \frac{\Gamma \left(n+ \frac{1}{2} \right)}{\Gamma \left(\frac{1}{2} \right)} \frac{1}{\Gamma(n+1)^{2}} \Gamma \left(n+ \frac{1}{2} \right) \\ &= \frac{1}{\pi a } \sum_{n=0}^{\infty} \frac{1}{n!} \frac{\Gamma \left(n+ \frac{1}{2} \right)^{3}}{\Gamma \left(\frac{1}{2} \right)} \frac{1}{\Gamma(n+1)^{2}} \, \left(\frac{4}{a^{2}} \right)^{m} \\ &= \frac{1}{a} \, {_3F_2} \left(\frac{1}{2}, \frac{1}{2}, \frac{1}{2}; 1,1; \frac{4}{a^{2}} \right). \end{align}$$
Therefore, for $a>2$, we have $$ \begin{align} \int_{0}^{\infty} J_{0}(ax) J_{0}(x)^{2} \, \mathrm dx = S_{2} &= \frac{1}{a} \, {_3F_2} \left(\frac{1}{2}, \frac{1}{2}, \frac{1}{2}; 1,1; \frac{4}{a^{2}} \right) \\ &\overset{(1)}{=} \frac{1}{a} \, {_2F_1} \left(\frac{1}{4}, \frac{1}{4}; 1 ; \frac{4}{a^{2}} \right)^{2}. \end{align}$$
But according to the Wolfram Functions Site, $$ {_2F_1} \left(\frac{1}{4}, \frac{1}{4}; 1; \frac{4}{a^{2}} \right) = \frac{2}{\pi } \, K \left( \frac{1-\sqrt{1- \frac{4}{a^{2}}}}{2} \right), $$ where $K(m)$ is the complete elliptical integral of the first kind with parameter $m=k^{2}$.
This identity provides the analytical continuation of $${_2F_1} \left(\frac{1}{4}, \frac{1}{4}; 1; \frac{4}{a^{2}} \right) $$ outside the unit circle.
It's then natural to wonder if this means that $$\int_{0}^{\infty} J_{0}(x)^{3} \, \mathrm dx \overset{?}{=} \Re \left( {_2F_1} \left(\frac{1}{4}, \frac{1}{4}; 1; 4\right)^{2} \right)= \frac{4}{\pi^{2}} \, \Re \left( K \left(e^{-i \pi/3} \right)^{2} \right). $$
A numerical approximation of the integral suggests that this is indeed true, which would mean that $$\Re \left( K \left(e^{-i \pi/3} \right)^{2} \right) = \frac{\pi^{2}}{4} \frac{\Gamma \left(\frac{1}{6} \right)^{2}}{2^{5/3} 3^{1/2} \pi^{3/2} \Gamma \left(\frac{5}{6} \right)}.$$
There is a proposal at the end of this paper to modify the rule that says that all divergent series should be discarded when using this method. I have yet to see see this discussed in other papers.
$(1)$ https://en.wikipedia.org/wiki/Clausen%27s_formula
Integrate[BesselJ[\[Nu], x]^3, {x, 0, Infinity}, Assumptions -> Re[\[Nu]] > -1/3]
. – Vladimir Reshetnikov May 28 '13 at 20:15