I am a big fan of base building and domain management type games. I assembled a list with help from the Something Awful traditional games board, of all the RPGs we could think of that had elements or full on rules of management types of games.
This list will be updated as needed. If a game line is listed (like Ars Magica) then these organizational rules are in the core book. Most of the others are supplements to major game lines, as these topics do not always get a central focus.
11/1/22 Edit: I've updated this list with additions from a Reddit thread on base building rpgs, here. Where possible, I have verified that these additional rpgs have base building rules.
4/20/23 Edit: Updated the list again thanks to another Reddit base building in rpgs thread, here. In addition I am using the excellent Realm-management wiki page from the Tabletop RPGs subreddit as a source for some of entries for this list.
D&D
Birthright (AD&D)
Stronghold Builder’s Guidebook (3.5 D&D)
Dragon 395 (4ed D&D) – strongholds and upgrades
Adventurer’s Vault 2; Dragon 383 – lair magic items
Dragon 412 (4ed D&D) – boats
Mordenkainen's Magnificent Emporium – hireling rules
Admiral o' the High Seas (4ed D&D; Pathfinder) aka Seas of Zeitgeist – building ships, naval combat
DMGR2 - Castle Guide for 2e AD&D
Strongholds & Followers (5e D&D)
OSR/D&D related
Ultimate Campaign (Pathfinder) – has updated Kingmaker rules
Hell’s Rebels Campaign (Pathfinder) – build a rebellion
Way of the Wicked Book 2 (Pathfinder) – Henchmen management rules
Way of the Wicked Book 6-7 (Pathfinder) – Kingdom management rules
The Nightmares Underneath - establishing ties to and influence over local businesses and organizations
Fields of Blood- The Book of War (d20)
Kingdoms: A Zine of Generational Proportions (OSR)
Sine Nomine (Kevin Crawford)
An Echo Resounding
Godbound
Stars Without Number
Other Dust
Silent Legions
HarnMaster
HarnManor – manage noble estate, growing motherfucking turnips
Pilot’s Almanac – sailing ships, trading cargo
White Wolf
Gilded Cage (V:tM)
Damnation City (V:tR)
Exalted 2e Storyteller's Companion – Mandate of Heaven rules.
Exalted 2e Masters of Jade
Traveller (Mongoose)
Traveller: Core – build planets
Merchant Prince - trading companies
Dynasty – manage dynasties over generations
Mercenary – military bases.
GURPS
GURPS Boardroom and Curia
GURPS Low-Tech Companions 1-3
GURPS Dungeon Fantasy: Taverns
GURPS Dungeon Fantasy: Guilds
GURPS City Stats
Forged in the Dark
Blades in the Dark
Wicked Ones (Free Edition)
Mountain Home
Powered by the Apocalypse
Apocalypse World - hardholder has to manage their settlement, the hocus has to manage their cult, the chopper manages their gang.
Stonetop
No Country for Old Kobolds
Solo
DELVE: A Solo Map Drawing Game
UMBRA: A Solo Game of Final Frontiers
Other
Base Raiders (Strange FATE) - p.187
Sagas of the Icelanders - Icelandic Homestead Management minigame
Mutant: Year Zero
Conspiracy X
Reign
Ars Magica
Pendragon
Gods and Monsters (Fate)
Mystic Empyrean
Legacy: Life Among the Ruins
Weapons of the Gods Companion
Green Law of Varkith (Dungeon World) – build guild
Spellbound Kingdoms
Savage Worlds Super Hero Companion – build superhero bases
Champions (all versions) – build superhero bases
Rogue Trader: Stars of Inequity – build planets and manage colonies
A Song of Ice and Fire (Green Ronin) – run game of thrones house and holdings
Dune: Chronicle of the Imperium – manage a House Minor
Dune (2d20): The Great Game: Houses of the Landsraad
Underground – changing society to be more or less crime-ridden rules
Conan the King (Modiphius) - see mostly chapter 8 about kingdom management and faction power struggles
Vaesen
Forbidden Lands
Twilight 2000 4th edition
Death in Space – spacecraft and space station rules
Shadows Over Sol: Siren's Call - systems for colony building, societal planning, advancement and mass combat.
Seeds of Wars - fantasy system agnostic rules for realm management and tactical warfare. Supposedly inspired by AD&D Birthright rules (above).
Sorcerers of Ur-Turuk – similar to Ars Magica, this rpg has rules for constructing a Vahnam, the home base for sorcerers and their staff.
Do Not Let Us Die In The Dark Night Of This Cold Winter – obtain and manage supplies for a doomed village
Lord Flataroys Guide to Keeps and Fortifications (Hackmaster 4e)
The Ultimate Base (Hero System)
Sanctum (Heart: The City Beneath) - focuses on supporting a base
Numenera: Destiny – has rules for GMing Communities
Warhammer Fantasy Roleplay 2nd Edition, Renegade Crowns – not a resource management game, but it provides background charts and tables for developing petty kingdoms and a simple system for resolving Internal and External problems for a realm.