Many of the games I'd suggest have already been related, but for one obscure title...

Demon's Rise: Lords of Chaos

"You are no hero … no prancing knight or scholarly wizard but a champion of the dark gods. As their chosen, you have command of legions of barbarians, beastmen and demons. Wield unholy strength, necromancy and hellfire to bring ruin to the civilized realms. Honor your gods on the bloody fields of battle in a quest for power and ascension.

Demon’s Rise: Lords of Chaos is a turn-based, tactical RPG set in a brutal and unforgiving fantasy world. Taking place amidst a horrific war in the cold north, the campaign will see your party fight innumerable enemies, huge monsters and powerful sorcerers. Victory will require the tactical use of terrain, morale, formations and magic. Build an increasingly powerful war band, command demonic allies, and crush those that stand against you."

Steam page: https://store.steampowered.com/app/844420/Demons_Rise__Lords_of_Chaos/

Hoping Wave Light Games might one day bring their whole catalogue of AA fantasy tactical turn-based games to GOG.

For "classic" (non moral-relative and post-fantasy etc.) "villain gameplay" you have Dungeon Keeper 1 & 2 and Overlord (not the animated series, even though it would fit).
From a morally relative or otherwise unhortodox perspective...well, like many have already said, you're always trying to rob the Dragon in its own lair after all: do you think it shouln't be pissed off?

Paper Sorcerer:
https://www.gog.com/game/paper_sorcerer

An homage to the already mentioned Wizardry IV (and other old-school dungeoncrawlers) and an extremely underrated and almost forgotten RPG.
Player controls an evil Wizard which must escape his prison, regain his powers, recruit a team of outcast creatures (witches, vampires, minotaurs, etc...) and fight the "Good Guys" who have imprisoned him.

Legend of Keepers: Career of a Dungeon Manager is similar to the aforementioned Iratus.

Obviously spoilers, but maybe Final Fantasy XII?

Spoiler tag that activates for people with the Barefoot Essentials script running in the browser:

[spoiler]

From what I remember of the game's plot, most characters aren't one dimensional, even most of the ones in the "villains' side". That means that even some of the bosses you get to fight are characters that would potentially be "good guys" given a bit of a push.
And there are even moments where one of the characters supposedly sided with villains uses diplomacy to stop issues that could end in deaths for both "sides".

[/spoiler]