Here are a few things for ideas for a game setting like the #Dungeon23 Ruby Base.
Villains & Vigilantes Island of Doctor Apocalypse
Mutants and Masterminds Island Lair GM guide and deluxe GM Guide – Island of Dr Sersei
The above is in the deluxe gamemaster’s guide as well – which has several supervillain lair archetypes which are quite good to borrow, with maps.
d20 – M&M 1e Headquarters & Hideouts – a couple of bits and pieces here
d20 – M&M 1e Headquarters & Hideouts 2
Champions – Island of Dr Destroyer
Savage World Supers – has a few base building notes.