LOTR info:
Mordor - A land/nation, not a city. However, there were some cities there. See below, you have some listed. Evil, Sauron/Orcs
Gondor - Same as above, a land/nation, not a city. Good. Men
Rohan - Same as above, a land/nation, not a city. Good, Men
Rhun - Same as above, a land/nation, not a city. No cities known here. Neutral/Evil, Menl
Rhovanion - A land, not a city. It's not even a nation, more like a part of a continent. (i.e. Central America)
Eriador - Same as above, a land, not a city. It's not even a nation, more like a part of a continent.
Lindon - A land/nation, not a city. However, there were some cities there. Good, Elves
Khand - A land/nation, not a city. Some cities there Evil, Men
Harad - A land/nation, not a city. Some cities there Evil, Men
The Shire - A land/nation, not a city. Good. Hobbits
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Minas Tinth - A city belonging to Gondor (Good)
Minas Morgul - A city belonging to Gondor (Good) in the Second Age (called Minas Ithil while Gondor had it.), and Mordor (Evil) in the Third Age.
Orodruin - Mt. Doom, a volcano. Belongs to Mordor (Evil)
Barad-dûr- A city belonging to Mordor (Evil). *Capital of Mordor.
Morannon - The Black Gate, a tower belonging to Mordor (Evil). Gondor (Good) captured it, but Mordor recaptured it when they took over Minas Morgul.
Edoras - A city belonging to Rohan (Good). *Capital of Rohan
Dol Guldur - A city belonging to Sauron (Evil). *Capital of Dol Guldur
Moria - Called Khazad-dûm, originally the Dwarves (Good) owned it, but it was later called Moria when the Balrog (Evil) took it over.
Erebor - The Lonely Mountain, and the city inside. Owned by the Dwarves (Good), then Smaug (Evil), and then the Dwarves (Good) again.
Isengard - A fortress city belonging originally to Gondor (Good), but later taken over by Saruman (Good -> Neutral -> Bad).
Rivendell - A city belonging to Elrond [Elves] (Good)
Bree- A city of hobbits and men belonging first to Arnor [Men] (Good), and then no-one but themselves when Arnor collapsed.
Mithlond - The capital of Lindon (Good)
Helms Deep - The fortress of Rohan (Good).
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If you need more city names, let me know, I'm working on a Middle-earth mod.