NP-hard problems on cographs
Perhaps my favorite open problem is of interest: the edge clique-cover problem on cographs. In the edge clique-cover problem, you want to cover the edges of the cograph with a minimal number of cliques. It is unknown if this problem is NP-complete.

To illustrate that the problem is probably hard, let $K_n^m$ be the complete multipartite graph with $m$ partite sets each of size $n$. This is a cograph. There exist $m - 2$ pairwise orthogonal Latin squares of order $n$ if and only if the edge clique-cover of $K_n^m$ is $n^2$. This was shown by Park, Kim and 
 Sano. This is a formula for the "cocktail party graph", that is, the case where $n = 2$.