Agreed with Fatebuoy on the overused part. Luthor and Zod are used a lot, but they're also just pretty great villain who mirror Supes in a really good manner. Darkseid has defiently been overrsatured in recent years for me, I might even say Brainiac, even though he hasn't been used nearly as often, just because I feel like he's scarcely been interesting since the 80s..
As for underused, I feel like Bruno Manheim became a much more obscure character in recent years despite being a pretty big name in the 90s and 2000s. I also wanna say Atlas and Vartox, but I feel that both of them would really lose their charm fi they were used super often. Terra-Man, the Pre-Crisis version, is defiently someone i'd love to see more again personally. I also fel lie you could bring back some of his silver/brone age villains like Amalak and Maaldor back in interesting ways.