Wow... I'll see what I can do.

This is going to be a long post...

Everything is divided into categories. Places, Organizations and Events first, then Regions, Towns, Areas, Waters and Locations for Places, Active and Inactive for Organizations, and Off-page, On-page, Greater and Lesser for Events. Towns includes cities and villages, and Locations is for specific buildings and landmarks. Acive and Inactive refers to organizations that are currently being used and ones that have never been used or are not being used currently. Question marks mean I'm not sure about something. I've excluded most people's houses, because they don't seem to be the most urgent things and their locations are very ambiguous, so keeping them in would make this way too long.

It's probably not the best arrangement, but I hope it helps.

Places

Regions

Central Kyngdom

Towns

-Olde Windswood

-New Windswood

-Fallen Heights

Areas

-Barelands

-Secret Forest 

-Great Forest

-mountains

Waters

-Wind Falls

-Lioncrook/Lioncreek Falls

-Two unnamed lakes west of Great Forest

-Eastern Estuary (unconfirmed, supposedly east of Meek Peak)

Locations

-Jolly Rancher (human inn above the Bog and Burrow Inn)

-Bog and Burrow Inn

-Meek Peak

-Bleak Peak

-B.I.G. headquarters

-Crunchtem Orphanage

-Knothole, Meek Peak

-Lycaella's house

-Nygrune's/Aris's house

-Laeta's house (or ex-house)

-the Clancy Orphanage

Southwestern Kyngdom

Towns

-Hidden Paradise Valley

-Sprocketville

-New Cogville

-East Wilton (unconfirmed)

Areas

-Green Hills

-Grasplands

-Labyrinth Lands

-Crimson Fields

-southwest coast

Waters

-Boiler Harbor

-Barrier River

-Clawmark River

Locations

-Brown Outpost

-Drifter Outpost

-Big Toe

-entrance to tunnels

-Charlie's house

-East Wilton Golden Elementary and Middle Schools (unconfirmed)

-Hidden Paradise Point (unconfirmed)

Eastern Kyngdom

Towns

-Rainefall

-Paralia

-East Whetston

-West Whetston

-An unnamed town north of Paralia

-Ferretsburg (unconfirmed)

      Areas

-Muddy Marshes

-Varie Badlands

-(south?)east coast

Waters

-Stagg...(map ends--Stagg-something River?)

-Hardswallow River

-Dagger Bay

-Numi Bay

-An apparently unnamed bay between East and West Whetston

-An unnamed river going through Paralia

-A something (aqueduct? Manmade river?) south of the Muddy Marshes

Locations

-Underwater Ball

-That unexplained giant purple tree thing

-Mrs. Monigan's Apartments

-Rebel Animal Academy?

-the Crying Caverns

Southeastern Kyngdom

Towns

-Aslahari (city, name translates to Desert Flower)

-Isti District

Areas

-Southern Deserts

-Sluella Swamps 

Waters

Unknown

Locations

-Sienna's home

-Arthi Manor (Nobyl Saralayah Pur Arthi's home)

Northern Kyngdom

Towns

-Adong District

Areas

-Barelands

Waters

Unknown

Locations

-Tangledclaw Middle School (Northwest Kyngdom)

Other/Unknown

Towns

-SailHaven

-Goldenfire

-Princeton (under a B.I.G. lab; Central Kyngdom?) 

-Tiln

-Forestia?

-Gear?

-Rune

-District AD?

-Marshtown

-Faltown (previously Dale County)

-Rushliville (eastern Kyngdom)

-Tumbling Pike (walled city)

-Sylvania?

-Little Human Hideaway

-Westminster

-Plotton

-Sparrow Valley?

-Jiffytown, Della

-Minktropolis

-Oakhome (in Oakheart Forest)

-Avalonia?

-Shoulder (western East Kyngdom)

-Outer Provinces? (walled something, probably city)

-Mer (town/city by the seaside and home to Harbor, who is a princess of it)

-The Nest, a village of upright catlike creatures in the northern forests

-Silvgo, another village of cat-people in the northern forests, only these cat people are the Dolor Felis

-Paralin/Paranli 

-Wind Falls, Kaualatin

-Starlight Stell, Kaualatin

-Frost'dulan, Kaualatin

Areas

-Terral forest, planet Zorrell

-Melancholy Moor

-Regalia?

-Lonelain Forest

-Mountains of the Sylvar Rocks

-Morbid's Forest

-the Pack Lands?

-the Maegin Mountains

-the Friendly Woods

-Swampy Grasslands

-Western Highlands

-Rocky Mountains

-the Hoofbeat Forest (home to Blazing Star, Guardian of the Power of Hoof)

-the Blue Mountains (probably near B.I.G. HQ)

-the Black Mountains

-Woods of Eternal Winter

-Forgotten Kingdom (Kyngdom?), Forbidden Lands

-Oakheart Forest (outside of the grasslands outside Cogville)

-a dark forest in Southern Kyngdom

-Dragon Country?

-Avalonia?

-Forest of the Sage

-Falling Leaves Rainforest

-Makengray Forest 

-the Æther Ruins

-the Smoke Mountains

-the Lilaani Woods (a country north of Kyngdom, open to Powers)

-UnderWorld? 

-the Gytralian Caves?

-Acnibaster Forest

-the Caves of Phosphor (cavern system beneath Kyngdom)

-the Mountains of Hoogaloogaloo

-Kaualatin, the underground land of pixies

Waters

-the River Shij

-the Healing Spring (guarded by Laya Diamondtail and her family)

-Secret Reef

-Musical Grotto (eastern Kyngdom?)

-Yaquina Bay

-the River of Silence

-Oceanus, Kaualatin

Locations

-Icy's house

-the Cypher Labs

-Booksy Owly's Animal Library

-The Great Pine (Scarletta's home)

-Clock Cave (Kathleen M.'s home, Northwest Kyngdom)

-Holt Stronghorn (Mere Bullbrook's home)

-The Library of Silver

-Reader's Barn (upstairs home to Wiseowl)

-Iron Mountain

-Crescent Island

-Azure Valley

-Red Trees?

-Moon Gazing Mountain?

-Man of the Moon Peak

-Plotton Elementary and High schools

-Sequoia National Park

-St. Lionel's Orphanage

-Shadow Moon Peak (home toSilverbeam, Guardian of the Power of Howl)

-The Pond On The West Side Of The Wall

-Della (an island off of Kyngdom's east coast)

-Nestling Orphanage (southern Kyngdom)

-the Hearth Hotel

-B.A.C. Housing Institute

-the Insect Orchestra Theatre

-Paradis Lodge (home to Lily Lotusweaver)

-Flicker Mountain

-Five Starfish Inn (possibly in underwater East Kyngdom)

-Dragon's Mouth?

-the Raven's Nest (???)

-the Island of Whispers (has something to do with B.I.G.)

-Fang Grotto (secret dragon haven in the mountains)

-Lamrin, an island where Kathleen the mapmaker lives

-Wensdun, another random island possibly not in Kyngdom

Organizations

Active

-the Brazen Inquiry Guild, or B.I.G.

-SOCS (Society Of Concerned Scientists)

-the FAFA (Fur And Feathers Association)

-Catastrophe's Army

-Elliot's Army

-Zhoulc's Army

-the Mutant Army

-the Elven Resistance

Inactive

-the Midnight Force

-Paige O'Booke's unnamed organization

-Alexander's Army

-First Order of Stealth

-Second Order of Stealth

-Third Order of Stealth

-the Estuary Guard

-the Morfordian Guard

-Kyngdom Music Conservatory 

-the Spy Guild

-Clan Luna

-Cap'n O (as far as I know)

-Sequoia Force

-B.A.C. (Bulwark (the) Animals Correlation)

-the Army of the Forest

-Morbid's Army

-Aliasa (underground trade/crime network, possibly still active)

And I'm going to have to save Events for some other time. The Story So Far threads should help with that for now, though.

I couldn't find any MAPMAKER'S ASSOCIATION thread, but I looked through the who's here? thread, along with several others.

This list may be incomplete even though I spent 7-8 hours on it, so if anyone knows of anything I missed, please tell me.