We consider generalized Paley graphs $Γ(k,q)$, generalized Paley sum graphs $Γ^+(k,q)$, and their corresponding complements $\bar Γ(k,q)$ and $\bar Γ^+(k,q)$, for $k=3,4$. Denote by $Γ= Γ^*(k,q)$ either $Γ(k,q)$ or $Γ^+(k,q)$. We compute the spectra of $Γ(3,q)$ and $Γ(4,q)$ and from them we obtain the spectra of $Γ^+(3,q)$ and $Γ^+(4,q)$ also. Then we show that, in the non-semiprimitive case, the spectrum of $Γ(3,p^{3\ell})$ and $Γ(4,p^{4\ell})$ with $p$ prime can be recursively obtained, under certain arithmetic conditions, from the spectrum of the graphs $Γ(3,p)$ and $Γ(4,p)$ for any $\ell \in \mathbb{N}$, respectively. Using the spectra of these graphs we give necessary and sufficient conditions on the spectrum of $Γ^*(k,q)$ such that $Γ^*(k,q)$ and $\bar Γ^*(k,q)$ are equienergetic for $k=3,4$. In a previous work we have classified all bipartite regular graphs $Γ_{bip}$ and all strongly regular graphs $Γ_{srg}$ which are complementary equienergetic, i.e.\@ $\{Γ_{bip}, \barΓ_{bip}\}$ and $\{Γ_{srg}, \barΓ_{srg}\}$ are equienergetic pairs of graphs. Here we construct infinite pairs of equienergetic non-isospectral regular graphs $\{Γ, \bar Γ\}$ which are neither bipartite nor strongly regular.