Greenvale - Deadly Premonition
There are a lot of things I would change about it and are probably due to a low budget but overall I enjoyed it for being a bit of a unique take on how towns in games are designed. Figuring out everyone's scheduled and where they would be at what time, nevermind some of the simpler things were a large part of the charm for me.
Santa Destroy - No More Heroes
Not exactly functional for much in itself, the cars and npcs barely offering interactivity and its purpose to just serve as a hub. Still I like the downtime it offered as well as a contrast to the fast stylized action. That and some of the "lore" about key locations, from lowlife dropouts to the military running top secret experiments, etc. Was disappointed to see it go in the sequel.
Zeal - Chrono Trigger
Overall due to the crazy reveal. Most towns up to this point were fairly standard for most RPGs. I like the theme going on of people becoming enlightened and all that just to have it all fall apart because their leader is corrupt with power.
Rogueport - Paper Mario 2
Not really the norm for a Mario game in general. Of course a lot of it is still played off as silly or dumb but I'd be hard pressed to find a noose anywhere else.
Liberty City - GTA4
As with many other aspects of V, the new version of Los Santos and how boring and unimaginative it is makes me appreciate 4 much more than I did when I'd been initially disappointed. It is largely more detailed, has less space wasted, a few more interiors, etc. Most of all the better driving physics make it fun to race around. Also the superior ragdoll physics.
Stillwater - Saints Row 2
Similarly Steelport was really not good at all. Though I wasn't initially disappointed by Stillwater either. It's not a huge world and maybe not so detailed in some ways but it has a ton of variety and builds off the previous game quite well.
Kamurocho - Yakuza series
Some versions are certainly better than others but overall it has been fun seeing how it's changed over the years. There have been other cities as well but I feel none are quite as developed unfortunately. At least from a visual standpoint I enjoyed the one Saejima went to in 5 but gameplay wise it was very basic.
Anywhere - EDF series
Because it's fun to blow everything up
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About suffering they were never wrong,
The Old Masters: how well they understood
Its human position; how it takes place
While someone else is eating or opening a window or
just walking dully along...