Though still primarily a human town, Ankh-Morpork on Discworld welcomes non-humans (dwarves and trolls mainly, but also Friendly Neighborhood Vampires, werewolves, the differently alive, a few banshees, gorgons, Igors, and Nobby Nobbs), or at least welcomes non-humans if they don't make trouble and have money to spend. There are troll neighborhoods, a bar just for undead and supernatural creatures, and it's technically the largest dwarf city on the Disc.
One novel of Vampire Hunter D features the town of the Barberois, a town of Half-Human Hybrids who are all part-monster (of many different monster types) and who can act as deadly mercenaries for the right conditions.
Mortasheen is one of these around the size of Austrailia, with a massive abundance grotesqueMons used for almost everything you can think of. Even your player characters are monstrous, with Mutants, Fish People, zombies, shadow-people, human-insect hybrids, morlocks that look like Orlock, and brain-in-a-jar styled cyborgs.
The Dungeons & Dragons setting of Eberron has several nations ruled by "monster" races: Darguun is the homeland of the goblins and hobgoblins, Q'Barra is settled by Lizard Folk, the Shadow Marches is one of the last holdouts of the orcs, Droaam is a safe haven for monsters of all kinds (from trolls to harpies to hags), the continent of Xen'drik is inhabited primarily by drow, giants, and various other exotic intelligent species, and Argonnessen is another continent completely ruled by prophecy-obsessed DRAGONS.
Examples of the Monster Town are quite common in the D&D Basic Mystara setting, both as independent states and as principalities within larger, multi-species nations.
The Underdark is controlled by multiple nations of drow, illithids, and other subterranean races, depending on the setting.
Tormenta, a Brazilian setting, has the "Dark Alliance" that rules the south continent, though most of their towns are conquered.
The late period GBC game Shantae had two settlements of this variety, referred to as Bandit Town and the Zombie Caravan.
Chrono Trigger had Medina Town, populated by the magical, monstrous Mystics (or Fiends). On your first few visits they're openly hostile, attacking you if you try to buy anything and then overcharging you horrendously once beaten, but it's possible to alter history by defeating the historical figures they idolize; if you do so, the monsters become much more hospitable because there wasn't anyone to build anti-human sentiment.
Chrono Cross had Marbule, a place where only Demi-humans lived.
Super Mario RPG: Legend of the Seven Stars contained Monstro Town, home of "reformed" monsters or plain fed up minions, including many of Bowser's henchmen from the beginning of the game
In the Paper Mario games this is taken even further: nearly every town has monster citizens, and nearly every species of monster will have at least one representative shown to be a harmless member of society, with the implication that there are more. Heck, the only evil monsters are ones aligned with Bowser, native monsters, or Chaotic Neutral monsters. In fact, this deserves its own page.
Monsters in the Final Fantasy Legend series (which were SaGa games, so this may also apply to SaGa as a whole) lived alongside humans so appeared both in the wild and in town. In the third game this was only true in the enemy's dimension of Pureland, though there were two classical Monster Towns along the way infested with random encounters and evil WaterHags and Dwelgs that will attack on sight if you are not disguised.
In Final Fantasy IV, there is a place hidden deep below the Underworld where the Summoned Monsters live. Rydia explains that this is where she's been living all the time that she was gone from the team. Various common monsters can be talked with and commerce proceeds as normal. Because they're Rydia's friends, they don't treat the party as enemies. However, one can get in fights. Specifically, the powerful summon monsters that Rydia has not yet formed a summoner's pact with, Asura and Leviathan, are willing to form such a pact with her if she and her friends can satisfy them in a test of combat.
InExcelsior Phase One Lysandia, for one quest you have to visit Grethal, populated by monsters of the same kind you spend the entire rest of the game killing. Oddly, they don't seem to mind.
Well-played in the Zelda-ish game Crusader of Centy, in which the plot slowly reveals that the Evil Monsters really aren't; they are the victims of human racism, and didn't want to be in the world in the first place. Eventually the protagonist enables them to leave, thus spelling utopia for both - and a very Family Unfriendly Aesop.
Dragon Quest VIII had Tryan Gully, which happens to be the only town in the game that your transformed companion Trode feels welcome in, as the monsters are not afraid of him like the humans in other towns are.
In Disgaea, this is essentially the whole Netherworld.
In Phantom Brave, there are several islands of anthropomorphic humanoids that also appear as enemies in the game.
In La Pucelle Tactics, the Eringas are a mushroom-like monster that you fight frequently, but you can also visit a town full of them that act perfectly friendly.
Baldur's Gate 2 had two examples of this: the first was an undead town in the sewers, although this is something of a subversion - if you go in they beg you to leave before their hunger overcomes them, then it does. The second is a collection of monsters living outside of a town. The mayor asks you to deal with them, and you have the option of killing them or talking to them and learning they just want to coexist. If you take the second option they start trading with the town and defend it when other monsters attack.
The Drow city, as well as the Mindflayer's domain southward of it.
Baldur's Gate also had that village of Xvarts, though they weren't too glad to see you.
Golden Sun: The Lost Age has a town full of werewolves, but they're not really mean to newcomers so much as they just go to massive efforts to hide the fact that they're anything besides human.
Plenty of examples from the Fallout series. Fallout has Necropolis, populated by friendly and feral ghouls. Fallout 2 has the towns of Broken Hills and Gecko, as well as the Deathclaw-occupied Vault 13. In Fallout 3 the non-feral ghouls of the DC area have set up Underworld in a museum on the national mall, while in Fallout New Vegas the former mayor of Broken Hills has founded Jacobstown, a pre-war ski resort he hopes other Super Mutants can turn into a peaceful community.
Po Po Lo Crois has one of these, once you get the Global Airship. Annoying in the PSP version, because there's literally nothing to do there. (The original PSX version had a tournament going on there in which you could win a power-up for Pietro.)
RuneScape has quite a few of these. Goblin Village, Barbarian Village (for a given value of "monster"), entire vampire and vampyre cities on the members' worlds...
World of Warcraft has plenty of monster towns, usually accessible after using a disguise and/or doing a reputation grind for the faction controlling the town: Magram and Gelkis Villages, Ogri'la, Dragonmaw Base Camp, The Shadow Vault, Dun Niffelem, Frenzyheart Hill, Mistwhisper Refuge, the Grim Guzzler and others. Of course, depending on your definition of monster, any settlement of Orcs, Trolls, Tauren, Undead, or Draenei can count.
Phantasy Star II has a whole planet of people who aren't exactly nice to you if you're wearing the wrong "cap"
Somewhat similar, in The Legend of Zelda: A Link to the Past, Kakariko Village is replaced with the Village of Thieves in the Dark World. It's filled with monsters that do indeed attack you, as well as fox-like people who you can play gambling games with.
Arguably, the Rogue Isles is the Monster Town to Paragon City in City of Heroes, being under the control of the evil organization Arachnos. Indeed, nearly all friendly NPCs are connected with Villain Groups in some way, or are generally just violent, greedy, or evil. (There are a few exceptions, like Ashley McKnight or Hardcase, but those are the exception rather than the rule.) However, despite all of this, 90% of the NPCs you will be facing are Villains. In fact, you will fight more Arachnos as a Villain than a Hero. Even if you work for them.
Every single town you visit in Ghosts N GoblinsRed Arremer/Gargoyle's Quest is a Monster Town. Naturally, since the setting takes place in the Demon World, which is under attack. You're a demon that goes around killing monsters, whereas the townspeople who are willing to help you out are monsters themselves.
The Mushroom Kingdom theme dungeon from MapleStory.
Legacy of Kain Soul Reaverreverses this trope. You play as an undead vampire-turned-wraith, Raziel. There is a hostile vampire hunter prior to the first boss which you can ignore or attack. After beating the first boss, you will be able to access the human settlement. If you chose to attack the vampire hunter, or if you choose to subsequently attack the citadel and its allies, the humans will be extremely hostile towards Raziel. If you chose to ignore him, the humans will begin to worship Raziel as their savior and even allow him to partially consume their souls if he's weakened.
Monster Hunter has the Melynx Villages where both Felynes and Melynxes hang out, and are one of the few place where the Melynxes don't actively try to steal your belongings. You can even find your purloined goods and retrieve them hassle-free, as well as some other goodies to make Barrel Bombs and a Barrel Lid to make a special weapon.
Planescape: Torment has the Dead Nations, a settlement inhabited by the undead - skeletons (intelligent and coherent), zombies (not very intelligent or coherent), and ghouls (craving for meat). They spend their days caring for the settlement and looking after the "quiet ones", i.e. inanimate corpses, to save them from desecration. When somebody living wanders into the Dead Nations, he is promptly captured and imprisoned; while the locals are treating him politely, they aren't trying to hide that they're merely waiting for him to die.
In Death Knights Of Krynn there's a town entirely populated by various types of undead that have built their town as a mirror of a normal, human town. Staying there is asking for all sorts of Random Encounters, as despite the welcoming words from the undead Mayor, you'll be attacked constantly should you stay.
In Annyseed there is a place where all the monsters can live their lives happily, away from humanity. To get there, just follow Reaper Road until it dips into the woodland, and when you come to a sign saying, "Skull Valley - no vehicles" just keep going a little further, until the undergrowth gets so dark you can hardly make out the road. But go at your own risk.
Early on in Looking for Group, Richard the undead Warlock claims to be the mayor of a village, which later turns out to be true. Said village is populated entirely by undead ghoul townsfolk who are virtually unkillable and almost as sociopathic as Richard. Luckily for everyone else, they appear amiable and cooperative when they aren't killing people or stealing babies...
Monster Isle in The Powerpuff Girls. Every so often, one of the locals goes out to fight the girls, and hopefully win. Whoever gets his ass kicked, and then comes back to tell them how awesome fighting them was, is considered a hero. And none of them see getting beaten black and blue by small, quasi-human girls as a problem.
Pixar's Monsters, Inc. has the protagonists (who are monsters) living in a monster town called Monstropolis, which most of the film takes place. The protagonists work at a power plant where they go through portals to bedrooms of human children (in an alternate universe, to produce electricity from the screams.) After the antagonistic owner of the company is defeated, the company makes the children laugh instead of scream in fear.