I believe the following gives the answer for $|G| = p^2q^2$, where $p,q$ are prime and $p < q$. I will use $f(p,q)$ to denote the number of groups of order $p^2q^2$.
a) $p=2$ and $q=3$: $f(p,q) = 14$.
b) $p=2$ and $q > 3, q = 3 \mod 4$: $f(p,q) = 12$.
c) $p=2$ and $q = 1 \mod 4$: $f(p,q) = 16$.
d) $p>2$ and $p \nmid q^2 - 1$: $f(p,q) = 4$.
e) $p>2$ and $p \mid q+1, p^2 \nmid q+1$: $f(p,q) = 6$.
f) $p > 2$ and $p^2 \mid q+1$: $f(p,q) = 7$.
g) $p > 2$ and $ p \mid q-1, p^2 \nmid q-1$: $f(p,q) = p + 10$.
h) $p > 2$ and $p^2 \mid q-1$: $f(p,q) = \frac{p^2+3p+24}{2}$.
Here's how I came up with these formulas:
Let $S_p$ and $S_q$ be $p$-Sylow and $q$-Sylow subgroups of $G$, respectively. Note that, except in the case $p=2$ and $q=3$, we have $q \nmid p^2-1$, so the group $S_q$ will be normal.
b) I: $S_q = \mathbb{Z}_{q^2}$
$\text{Aut}(S_q) = \mathbb{Z}_{q^2}^* \approx \mathbb{Z}_{q^2-q}$, and $q^2-q$ is divisible by $2$ but not $4$. If $S_p = \mathbb{Z}_4$ then we can either have a generator of $S_p$ act on $S_q$ via the unique involution, or it can act trivially, resulting in two groups. If $S_p = \mathbb{Z}_2 \times \mathbb{Z}_2$, then either two of the elements of $S_p$ can act on $S_q$ via the involution and two act trivially, or they can all act trivially, resulting in another two groups.
II: $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$
$\text{Aut}{(S_q)} = \text{GL}_2 (F_q)$, which is a group of order $q(q+1)(q-1)^2$. If $S_p = \mathbb{Z}_4$, let $g$ be a generator of $S_p$. There are elements of order $q+1$ in $\text{GL}_2 (F_q)$, and $q+1$ is divisible by $4$, so we can map $g$ to an automorphism of order $4$. It turns out that this yields a unique group up to isomorphism. Otherwise, the action of $g$ on $S_q$ will have two eigenvectors $u$ and $v$. The action on $u$ will be an action on the subgroup $\mathbb{Z}_q$ generated by $u$; since $q-1$ is not divisible by $4$, the action must be the unique involution or the trivial action. So the action of $g$ can either act nontrivially on both of $u$ and $v$, just one, or neither, adding another three groups. (To see that acting on both vectors yields a different group than acting on one, observe that the first fixes only the identity, whereas the latter fixes either $u$ or $v$.) If $S_p = \mathbb{Z}_2 \times \mathbb{Z}_2$, then we have two independent vectors $a$ and $b$ in $S_p$, and for each we have three different possible actions. Suppose at least one acts trivially; then the other has three possible actions, yielding three more groups. Finally, if no nonidentity element of $S_p$ acts trivially, then there is one possibility: one element acts nontrivially on $u$, one on $v$, and one on both $u$ and $v$. This yields the final group.
All told there are 12 groups up to isomorphism.
a) We have $p=2$ and $q=3$. The 12 groups described above all exist in this case as well, but there is also the possibility that $S_q$ is not normal, since $q \mid p^2-1$. One can show that if $S_q$ is not normal, than $S_p$ will be. If $S_p = \mathbb{Z}_4$, then $\text{Aut}(S_p) = \mathbb{Z}_2$, so $S_q$ cannot act nontrivially, so it would be normal. So we must have $S_p = \mathbb{Z}_2 \times \mathbb{Z}_2$. In this case we have $\text{Aut}(S_p) = S_3$ (the symmetry group on three elements, in this case the three nonidentity elements of $S_p$). If we have $S_q = \mathbb{Z}_9$, then we a unique group where $S_q$ acts nontrivially on $S_p$. Similarly for $S_q = \mathbb{Z}_3 \times \mathbb{Z}_3$. The reason is that $S_q$ must map to the subgroup $\mathbb{Z}_3$ of $\text{Aut}(S_p)$, and in both cases there is only one way to make such a mapping up to isomorphism.
This adds two more groups for a total of 14.
c) $p=2$ and $q = 1 \mod 4$. Again we have the 12 groups described in section b). We also get additional groups in the case $S_p = \mathbb{Z}_4$. When $S_q = \mathbb{Z}_{q^2}$, we get one group where a generator for $S_p$ maps to an automorphism of $S_q$ of order $4$; this exists since $4 \mid q^2-q$. When $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$, one of the basis vectors for $S_p$ can map to an automorphism of order $4$ (guaranteeing new groups) and the other can map to automorphism of either order $1,2,$ or $4$, yielding 3 new groups.
This adds four groups for a total of 16.
d) If $p \nmid q^2 - 1$ and $q \nmid p^2 - 1$, then both Sylow subgroups are normal, and the group is just the direct product of the two. There are two possibilities for each Sylow subgroup, yielding 4 groups in total.
e) If $p \mid q+1$ but $p^2 \nmid q+1$, then we still have the $4$ groups from d). We get no new groups when $S_q = \mathbb{Z}_{q^2}$, since $p \nmid q^2 - q$, however if $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$ then we get $p \mid |\text{Aut}(S_q)| = q(q+1)(q-1)^2$, so by Cauchy's theorem there are elements of order $p$. So we get one group with $S_p = \mathbb{Z}_{p^2}$, and one group where $S_p = \mathbb{Z}_p \times \mathbb{Z}_p$.
This adds two groups for a total of 6.
f) If $p^2 \mid q+1$, we still have the 6 groups from e), and we also get one group where $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$, and $S_p = \mathbb{Z}_{p^2}$, and a generator for $S_p$ maps to an automorphism of $S_q$ of order $p^2$.
This adds one group for a total of 7.
g) I: $S_q = \mathbb{Z}_{q^2}$.
If $S_p = \mathbb{Z}_{p^2}$, then a generator for $S_p$ can either map to an automorphism of order $p$, or to the identity, yielding two groups. If $S_p = \mathbb{Z}_p \times \mathbb{Z}_p$, then either two of the elements of $S_p$ can map to an automorphism of order $p$ and the other two to the identity, or they all can map to the identity, yielding two more groups.
II: $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$.
If $S_p = \mathbb{Z}_{p^2}$, then a generator for $S_p$ will map to an automorphsim of order $p$ or $1$. Such an automorphism $g$ will have two independent eigenvectors $u$ and $v$. Suppose that $g$ fixes neither $u$ or $v$. If $a$ is an element of order $p$ in $\mathbb{Z}_q^*$, then $g$ will map $u$ to $a^i u$ and $v$ to $a^j v$ for some $ I,j$ between $1$ and $p-1$. Then $g^k$ will map $u$ to $a^{ik} u$ and $v$ to $a^{jk} v$, so we can choose $k$ so that $a^{ik} = a$. This will make $g^k$ a mapping from $u$ to $au$ and $v$ to $a^l v$. So there appear to be $p-1$ possibilities. However, we can also choose $k$ so that $a^{jk} = a$, so that $g^k$ maps $u$ to $a^m u$ and $v$ to $av$. This obviously yields an isomorphic group to the case where $g^k$ maps $u$ to $au$ and $v$ to $a^m v$, since we can just switch $u$ and $v$. So we wind up with pairs $(l,m)$ where either choice results in the same group. There are two cases where $m$ and $l$ are the same, namely $m = 1$ and $m = p-1$; the remaining $p-3$ numbers divide up into pairs, resulting in $\frac{p-3}{2}$ different groups, then the cases $m=1$ and $m=p-1$ add two more groups. Finally there is the possibility that $g$ fixes at least one of $u$ or $v$. We can either have $g$ move one, or have $g$ act trivially on both, yielding two more groups for a total of $\frac{p+5}{2}$ under this case.
If $S_p = \mathbb{Z}_p \times \mathbb{Z}_p$, then first consider the case where one of the basis vectors of $S_p$ acts trivially on $S_q$. Then the other cases can act in any of the $\frac{p+5}{2}$ ways above, adding that many new groups. Otherwise, we must have every nontrivial element of $S_p$ act nontrivialy on $S_q$; there is really only one possibility, where one basis vector moves some eigenvector $u$, and the other basis vector moves an independent eigenvector $v$.
In total, there are $p + 10$ different groups.
h) I: $S_q = \mathbb{Z}_{q^2}$.
We get four groups as in g). However, in the case that $S_p = \mathbb{Z}_{p^2}$, we also get a group where a generator for $S_p$ maps to an automorphism of order $p^2$, as $p^2 \mid q^2 - q$.
II: $S_q = \mathbb{Z}_q \times \mathbb{Z}_q$.
First, suppose that $S_p = \mathbb{Z}_p \times \mathbb{Z}_p$. Then we get the same $\frac{p+7}{2}$ groups as listed above in g). Next, suppose that $S_p = \mathbb{Z}_{p^2}$. Again, let $g$ be a generator for $S_p$, and let $u$ and $v$ be independent eigenvectors under the action of $g$. If $g$ maps to an automorphism of order $p$ or $1$, then we will get one of the $\frac{p+5}{2}$ groups listed in g). If $g$ maps to an automorphism of order $p^2$, then it must perform an action of order $p^2$ on either $u$ or $v$; WLOG suppose the action on $u$ is of order $p^2$. We get one group where $g$ acts trivially on $v$. Suppose the action on $v$ is of order $p$; then, if $a$ is an element of order $p^2$ and $b$ an element of order $p$ in $\mathbb{Z}_q^*$, we can choose $k$ so that $g^k$ takes $u$ to $au$ and $v$ to $b^m v$, where $m$ can be any number from $1$ to $p-1$. This leads to $p-1$ different groups. (No pairing this time since we can distinguish $u$ and $v$) Finally, suppose the action on $v$ is of order $p^2$. Then, as we have argued previously, we can choose a $k$ such that $g^k$ maps $u$ to $au$ and $v$ to $a^l v$, where $l$ can be any of the $p^2 - p$ elements of $\mathbb{Z}_{p^2}^*$. As before, the elements will be paired off, except for $l =1$ or $l =p^2-1$. So this results in $\frac{p^2-p+2}{2}$ possible groups.
All told, there will be $\frac{p^2 + 3p + 24}{2}$ different groups.
CallWithTimeout
- see the pre-release announcement here. I will check the workspace question - not sure at the moment. Please remind me next week if I will not get back to you earlier. $\endgroup$