We know, or have a good idea, why a number of locations belonging to or named by rabbits were named what they were:

• Immovable Mountain: was a mountain that, unusually enough for a mountain, apparently didn't move. Except for the one time it did. Which is the event in the mountain's history that gets brought up most. Weird.

• Blue Moss Hills: from a distance, looked like they were covered in blue moss. Only, as it turns out, they were actually covered in standard colored moss and blue flowers.

• Mistenlands: were...misty. Very misty.

• Golden Coast: was a coastline where rabbits found gold.

• Seddleton: named after Seddle.

• High Bleaks: mountains that are high...and bleak.

• Low Bleaks: smaller mountains right next to the High Bleaks.

• Kingston: named after King Whitson.

• River Flint: named after Flint

• River Fay: named after Fay.

• Halfway Harbor: was a harbor that was hoped to be the symbolic halfway point of the journey of Whitson's community.

• Grimble Island: an island best known for its association with the Grimble family. A bit awkward when you consider that the patriarch of the family was killed (and presumably eaten) there.

• Lener's Crossroads: a camp turned settlement near a crossroads found by a fellow named Lener Spry.

• Dragon Mountain/Forbidden Island: initially the mountain headquarters of the dragon species. Later an island that folks were forbidden to visit.

• Great Wood: a wood…that was pretty great, I guess.

• First Warren: the capitol of rabbit civilization in Natalia, originally an actual underground warren. First here is in terms of prominence, rather than chronology, since Kingston could be said to hold that honor at least in terms of longevity.

• East Wood: a wood that’s east of west wood, but north of the Great Wood.

• West Wood: a wood that is west of East Wood.

• Goforth River: a river that flows forth from First Warren's Lake Merle.

• Blackstone: near Black Lake...though we don't know why the lake is called that.

• Red Valley: near Red Lake...don't know why that lake is called that either.

• Decker's Landing: a landing that belonged to a guy named Decker.

• Cloud Mountain: a mountain...with clouds.

• Chelmsford: apparently named for a rabbit clan of Whitson and Lander's day known as the Chelms. Also quite close to the Goforth River, and so probably near a ford.

However, there are a number of locations that we don't know the in-universe origins of names for:

• Corby

• Glen Clair

• Lake Merle

• Natalia

• Nick Hollow (I've seen it proposed that it may be named for Nickel Drekker, but so far we have no confirmation)

• Halfwind

• Harbone

• Vandalia (though we do know that S. D. Smith is quite fond of what was a proposed name for his home state of West Virginia)

• Witmer River

I think I covered all the most notable ones. I didn't include Akolan since for all we know that's a Preylord name.