Pretty much the oldest cliché in the Big Book of Being a Bad Guy is to build your immense, trap-filled lair forever downwards, letting adventurers get deeper and deeper under the Earth's crust as they contemplate how great an idea following this dark pit into Hell was. Slightly less common is the opposite scenario: An immense tower that stretches into the sky and tests your resolve in other ways. Chiefly, it tests just how athletic you are and how comfortable your footwear really is after fifty flights of stairs, and how impressively vertiginous the vistas will be at the top where there's probably going to be a boss fight with a dragon or some giant asshole bird to obstruct the view.
The below is a rather tall (it seemed germane) list of towers in video games. Rather than check JRPGs-R-Us for every single instance of a tower dungeon, I've just given you something of a sampler of the interesting variations you're likely to find.
But then, this list is no match for my Glower Power. Oh, there's still a moratorium on Simpsons references? Tch, you're all impossible.