What are the subgroups of the semidirect product of the elementary abelian group of order 8 by $S_3$?
This is the group $(\mathbb{Z}_2\times \mathbb{Z}_2\times \mathbb{Z}_2)\rtimes S_3$ of order 48; $S_3$ acts on the elementary abelian $2$-subgroup by permuting three copies of $\mathbb{Z}_2$.
(i.e. if $\langle a_1\rangle \times \langle a_2\rangle \times \langle a_3\rangle$ is the elementary abelian $2$-group, and $\sigma\in S_3$, the action of $\sigma$ on the elementary abelian $2$-group is $\sigma (a_1^{\epsilon_1} a_2^{\epsilon_2}a_3^{\epsilon_3})\sigma^{-1}=a_{\sigma(1)}^{\epsilon_1} a_{\sigma(2)}^{\epsilon_2}a_{\sigma(3)}^{\epsilon_3}$ and $\epsilon_i\in\{0,1\}$.
[Unfortunately, I don't have GAP.]
The comments specify that the question is specifically for subgroups of order 24. An explicit calculation shows that there are three such subgroups:
In the classification of transitive groups of degree 3 (your group is a wreath product $C_2\wr S_3$) from http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6560180&fileId=S1461157000000115
they are groups number 6,7 and 8, respectively.