command and conquer
civilisation series
fallout series (fat man/mini-nuke, also you can detonate the unexploded nuke in fallout 3)
earth defence force series (i’m pretty sure there’s a tactical nuke for the pale wings unlocked pretty late on)
i think r-type final and/or tactics might have at least one nuclear-equipped ship?
dredmor has a throwing weapon named only The Bomb, its description is a very clear reference to it being a nuclear bomb. on hit, it actives a spell titled ‘They Blew It Up.’ you can get one free by maxing the Communism skill tree
in one must fall battlegrounds you are a giant robot and you can pick up a nuke and throw it at other giant robots
shadow warrior had a nuke that was a lot fun to use to wipe out large groups of rabbits
unreal had the redeemer. there was a dr strangelove mod where you could ride the redeemer around the level like a spaceship, then hop off once you wanted it to fly forwards and blow up. it was rad.