I've always enjoyed this trope, so I figured I'd share a few examples and see if there were any I'm missing.

Diamond Dogs by Alastair Reynolds
This is a short story, more sci-fi than fantasy, but one of my favorites. There's a mysterious alien tower on an empty planet. As the explorers arrive, they notice a number of remains of previous expeditions.

The tower requires them to solve puzzles to continue to advance. The higher they go, the harder the puzzles and the more difficult the structure is to maneuver. Without spoiling too much, they have to continually modify and change their bodies in order to progress in the tower.

Senlin Ascends by Josiah Bancroft
This is a pretty popular book around here, but to give a brief synopsis, there is a giant Tower of Babel. Senlin, a schoolteacher, is visiting with his wife when they get separated and he has to ascend the tower in order to find her.

Sufficiently Advanced Magic by Andrew Rowe
Great example of /r/ProgressionFantasy and a coming of age novel. When children are old enough, they enter into the tower for a trial that grants them an "attunement," which is basically a magic class/power. There are a number of towers spread throughout the world and each one is ruled by a god.

The Salamanders by JackWake
Fair warning, this is a web serial, but I think it's really good. Very similar to Sufficiently Advanced Magic. It follows two best friends, Ryan and Micah, as they explore the tower, level up, and join the Climber's Guild. All this takes place in the backdrop of the tower changing in ways that no one yet understands.