The most common alternative I have seen is a massive underground labyrinth. But that's really just one big, linked (sometimes alive) dungeon.

For something actually unique... hmmm.

What about subworlds? A "main world" can invade weaker planes of various sizes. The big thing about subworlds, is that they are entire worlds, with living sapient inhabitants. Dungeons and towers sometimes don't have any sapient inhabitents but boss monsters and the "players".

Some tower fantasy manhwa have each floor with sapient inhabitants, but I would argue that subworlds are different, because subworlds can't interact with eachother the way tower floors can. There is no "higher floor power puppets powers on lower floors" because subworlds can't talk to eachother, other than the most powerful worlds which wield dimensional transportation magic/technology.

The other interesting thing about subworlds, is that you could have them have unique magic systems per subworld, forcing adaptation from the main character. Characters could also bring some of this special magic back to their main world.