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 previously evaluated an integral using this method 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 associated 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 $$ \begin{align} \int_{0}^{\infty} J_{0}(ax) J_{0}(x)^{2} \, \mathrm dx = S_{2} &= \frac{1}{a} \, {_3F_2} \left(\frac{1}{2}, \frac{1}{2}, \frac{1}{2}; 1,1; \frac{4}{a^{2}} \right) \\ &\overset{(1)}{=} \frac{1}{a} \, {_2F_1} \left(\frac{1}{4}, \frac{1}{4}; 1 ; \frac{4}{a^{2}} \right)^{2} \\&\overset{(2)}{=} \frac{1}{a} \, {_2F_1} \left(\frac{1}{2}, \frac{1}{2}; 1 ; \frac{1-\sqrt{1- \frac{4}{a^{2}}}}{2} \right)^{2} \\&= \frac{4}{\pi^{2} a} \, K \left( \frac{1-\sqrt{1- \frac{4}{a^{2}}}}{2} \right)^{2}, \end{align}$$
where $K(m)$ is the complete elliptical integral of the first kind with parameter $m=k^{2}$.
$(1)$ https://en.wikipedia.org/wiki/Clausen%27s_formula
$(2)$ https://dlmf.nist.gov/15.8#E18
The above formula doesn't hold for $a=1$.
But what appears to be true is that $$\int_{0}^{\infty} J_{0}(x)^{3} \, \mathrm dx \overset{?}{=} \frac{4}{\pi^{2}} \, \Re \left( K \left(\frac{1-i\sqrt{3}}{2} \right)^{2} \right). $$
And if this is true, then $$\Re \left( K \left(\frac{1-i\sqrt{3}}{2} \right)^{2} \right) \overset{?}{=} \frac{\pi^{2}}{4} \frac{\Gamma \left(\frac{1}{6} \right)^{2}}{2^{5/3} 3^{1/2} \pi^{3/2} \Gamma \left(\frac{5}{6} \right)}.$$
Integrate[BesselJ[\[Nu], x]^3, {x, 0, Infinity}, Assumptions -> Re[\[Nu]] > -1/3]. – Vladimir Reshetnikov May 28 '13 at 20:15