I was about to mention Eberron as a good example of cosmology that matters.
@Aldarc mentioned Dollurh's effect on various religions, but you also have manifest zones where planar influence creates regions that are basically a form of natural resource – for example, Sharn's towers rely on the planar influence of Syrania, and Karrnath makes use of Mabaran manifest zones to enable them to create their special undead types. Of course, you could just say that these are "leyline confluences" or whatever, but linking them to planes gives them some more depth.
It’s interesting how different things appeal to different people. I was not even aware of the Mabaran Karrnath thing but that is a good leveraging of both. I was aware of the Sharn connection, but as you say flying cities exist in other settings like Golarion and the Forgotten Realms from ancient magically powerful empires.
Manifest zones and planar conjunctions are good opportunities to explain specific themed phenomena and sorcerers and such.
I couldn’t list more than a few of Eberron’s (13?) planes though and their associations without looking them up. Death, madness, dream, air? The Eberron planes just did not hook my interest.
For me the really engaging part of the Eberron cosmology is the 3e clerics of any alignment for any religion and the reality of the gods being theoretical is the cool part. It matches my own 3e and on campaigns’ divine casters are a spell casting tradition that taps divine power directly and not granted by gods.
This cosmology is very Conan, spell casting priests and intense present religions but the gods may or may not exist.
It allows many types of religion such as the Blood of Vol or elven ancestor worship or traditional D&D polytheism or even Buffy the Vampire Slayer Watcher style non religious secret societies with a spell casting tradition.
It allows many types of druids as nature worshippers or nature god followers or Shub-Niggurath mythos cultists or Merlin style magicians or Ars Magica Bjornaer mages.
It allows medieval church themes and story plot lines such as heresies and schisms, and corrupt priests or inquisitions in a good church.
It allows religions of false gods to be plausible in the D&D setting and allow cults to develop around powerful beings like fiends or angels or giants and dragons.
It allows different styles of real gods. Was Zeus a mortal king who was euhemerized, a storm giant, an embodied Olympian who exists with 1e style stats, a remote conceptual being greater god like in 2e who can project an avatar, or an entirely made up myth?
I really like the Silver Flame and Blood of Vol and different factions of druids and varied Khyber cultists.