Holy City: For the Empire, Ellenith, the holy city which serves as the center for the Church of the Flame, being built around the Dome of Unity, the 6th of the temples along the Shining Path, the seeress Merriéle‘s path to her conversation with the gods atop the mountain Tirias Calémon. (One might also consider other locations relevant to her life as this, save for the small problem that her birthplace isn’t actually known, and the place of her death no longer exists due to the, ah, explosive circumstances of same.)
It is a particularly holy city, of course, because the whole city is one giant temple, constructed as a giant engraved celestial mandala with all secular functions banished to the towns and villages inside the Deeping, yet outside its precincts. While it does house some indirectly theological function, it’s clearly dominated by its temples and shrines (every accepted order has at least one here), its libraries, and by such other special hallows as the Vaults of Earth and Water, the Hall of Chained Gods, and so forth.
(Depending on how you look at it, you might also be able to consider the Deeping as a whole – fields, forests, towns, and all – as an example of this category: it’s located in an ancient astrobleme, and the entire rim has been carved into a labyrinth, with all manner of vaults, halls, and curiosities hidden therewithin, even aside from its defensive function.
The larger Ledges of the Dead almost certainly also fall into this category.)