Off the top of my head:
All the gatetowns, some larger than others.
Grenpoli - the 'City of Diplomacy' in Baator
Jangling Hiter - Kyton capital city / home to most of their kind
Center - trade city located at the triple tangent point of the three Glooms of the Gray Waste
Portent - city in Gehenna in which overt violence is turned upon the perpetrator
Corpus - city in the Waste
Khin-Oin - yes it's a tower, but it's larger than virtually any city on the planes with the sole exception of Malsheem
Death of Innocence - city in the Waste that's a bit of a safe area from the Grays
Nimicri - living moon/trade city that floats above Gehenna. Most of the inhabitants of the city are exuded and controlled by the city itself. Occasionally it devours visitors who can add to its collection of residents once it devours them and gains their skills and memories, etc.
Release-From-Care - Guardinal city located near the portal from Ecstasy
Grandfather Oak - city in Arborea that sprawls along the base and branches of a single massive tree
The Pinwheel - stable spot of earth in limbo, touched by a branch of Yggdrasil
The Floating City - religious capital of the githzerai of Limbo (home of Zaerith Menyar Ag Gith)
Shrak'kat'lor - military capital of the githzerai of Limbo
The Citadel of Ice and Steel - Djinn capital city in Elemental Air
The Great Dismal Delve - primary region of Dao occupation, a bit spread out to call a city however
City of Brass
City of Glass
The Citadel of 10000 Pearls - Marid capital city
The Fortress of Life - small, shielded keep in Positive energy
Deathheart - big spherical city in Negative Energy, overrun with undead
Fortress of the Soul - primary residence of the Dustmen faction outside of Sigil
Gnome's Home - small pocket of quasielemental mineral that floats within paraelemental ooze, contains a small population of gnomish miners who have secured and adapted to their new environment
The Hidden City - small human floating city in paraelemental smoke, warded from detection and from the atmosphere, Ehkahk is hunting for the place with little luck
The Eye - village atop a small hunk of elemental earth floating in a storm-free spot in quasielemental lightning. Shows blatant signs of having been constructed by a very powerful spellcaster.
The Kingdom of the Blind - refugee/exile kingdom contained within a drifting mineral geode tumbling through quasielemental radiance. Ruled by a tiefling whose spirit was infused into a golem.
The Refuge of Color - only natural solid ground in quasielemental radiance. The 'city' is home to flocks of Varisoh, and the enigmatic, god-like King Black and Queen White (hawk headed 10ft tall humanoids of unknown origin)
Adrift - city built in a 1 mile wide ring in quasielemental steam. The hollow point of the ring is filled with the massive, drifting statues of the city's founders
The Quasielemental Doomguard fortress-cities:
The Crumbling Citadel (ash)
Citadel Sealt (salt)
Citadel Alluvius (dust)
Citadel Exhalus (vacuum)
Citadel Cavitius - former deific domain of Vecna, before that a former stronghold of the Doomguard. Current status questionable since Vecna's temporary stint in Ravenloft, and subsequent return. Most likely abandoned to the (quasi)elements, potentially reclaimed by the Doomguard splinter sect in that (quasi)plane.