I've attempted to compile as complete of a list as I can here:
Setting GuidesD&D v.3.0Freeport: The City of Adventure (2002)
SystemlessThe Pirate's Guide to Freeport (2007)
Cults of Freeport (2007)
Buccaneers of Freeport (2008)
Freeport CompanionsTrue20 Freeport Companion (2007)
d20 Freeport Companion/3rd Era Freeport Companion (2008)
Castles & Crusades Freeport Companion (2008)
Savage Worlds Freeport Companion (2008)
Wizards & Warlocks (Mutants & Masterminds; 2009)
Freeport Companion (4th Edition D&D; 2010, Expeditious Retreat Press)
Freeport Companion: Pathfinger RPG Edition (2010)
AdventuresD&D v.3.0The Freeport Trilogy:
-- Death in Freeport (2000)
-- Terror in Freeport (2000)
-- Madness in Freeport (2001)
Freeport Trilogy web enhancements:
-- Reikert Lloyd, Captain of Verlaine's Guard (Focus on Freeport #3; 2001)
-- The Captain's Council (Focus on Freeport #4; 2001) [Madness preview]
-- The Temple of the God of Knowledge (Focus on Freeport #6; 2001)
-- The Jade Serpent (Focus on Freeport # 7; 2001)
Holiday in the Sun (Focus on Freeport #5; 2001)
Hell in Freeport (2001)
Hell in Freeport web enhancements:
-- Hell's Foes (Focus on Freeport #9; 2001)
-- Hell in Freeport Prestige Classes (Focus on Freeport #9; 2001)
Deus Ex Machina (Focus on Freeport #11, 13, 14; 2001-2002)
The Consequence of Vice (ENWorld Players Guide #1, 2002)
Tales of Freeport (2003)
D&D v.3.5Black Sails Over Freeport (2003)
Sons of the Sea (ENWorld Players Journal #1, 2002) [for Black Sails]
Dead Man's Quest (Dungeon #107/Polyhedron #166, Feb. 2004; Paizo Publishing)
The Freeport Trilogy:
-- Death in Freeport Revised (2004)
-- Terror in Freeport Revised (2004)
-- Madness in Freeport Revised (2005)
-- The Freeport Trilogy: Five Year Anniversary Edition (2005)
Shadows in Freeport (Dungeon Crawl Classics #20; 2005, Goodman Games)
Vengeance in Freeport (2005, Ronin Arts)
Crisis in Freeport (2006)
Gangs of Freeport (2006, Adamant Entertainment)
Dark Wings Over Freeport (Bleeding Edge Special; 2007)
Blood of Freeport (2008, Adamant Entertainment)
PathfinderPeril in Freeport (2011, Adamant Entertainment)
True20Death In Freeport: A True20 System Starter Adventure (2006)
Dark Wings Over Freeport (Bleeding Edge Freeport Special; True20 Appendix; 2007)
True20 Freeport: The Lost Island (2009)
Multiple SystemsFury in Freeport (in various Freeport Companions)
Other SupplementsSystemlessPlayer's Map of Freeport (Focus on Freeport #12; 2001)
Freeport Adventure Hooks (2005)
Freeport Poster Map (2008)
Reading the Skull and Crossbones (2008)
D&D v.3.0Falthar's Curios (Focus on Freeport #1; 2000)
The Freeport Pirate (Focus on Freeport #2; 2000)
An Unwelcome Guest (Focus on Freeport #8; 2001)
Firearms in Freeport (Dragon Magazine d20 Special, 2001 Annual; Paizo Publishing)
Salon du Masque (Focus on Freeport #15; 2002)
Denizens of Freeport (2003)
Denizens of Freeport Web Enhancement (2002)
D&D v.3.5Creatures of Freeport (2004)
Creatures of Freeport Web Enhancement (2004)
Treasures of Freeport (2005, Ronin Arts)
Freeport's Temple Quarter (web enhancement for Temple Quarter; 2005, The Game Mechanics)
Cults of Freeport 3rd Era Web Enhancement (2010)
Buccaneers of Freeport 3rd Era Web Enhancement (2011)
D&D 4eUsing the Pirate's Guide with 4e (Freeport news feed, 2008)
Dragon AgeFreeport Backgrounds for Dragon Age (Kobold Quarterly 13, Spring 2010; Open Design)
True20Cults of Freeport True20 Web Enhancement (2010)
Buccaneers of Freeport True20 Web Enhancement (2011)
WFRPGrim and Perilous Freeport (Freeport news feed, 2007)
The World of FreeportD&D v.3.0Monsters of the Mind (2003) [Naranjan]
Mindshadows (2003) [Naranjan]
D&D v.3.5Egyptian Adventures: Hamunaptra (2004)
Exile (2005) [Hamunaptra]
Corwyl: Village of the Wood Elves (2005)*
Dezzavold: Fortress of the Drow (2005)*
Bleeding Edge Adventures [in and around Ivory Ports]:
-- #1: Mansion of Shadows (2006)
-- #2: Beyond the Towers (2006)
-- #3: Dirge of the Damned (2006)
-- #4: A Dreadful Dawn (2007)
-- #5: Temple of the Death Goddess (2007)
-- #6: Escape from Ceranir (2007)
[*I don't own these two books, but Cults of Freeport references Dezzavold, which is a companion book to Corwyl.]
Short Fiction"A Sailor's Tale" (Gaming Frontiers #2, Feb. 2002)
"Bury Me in Freeport" (Gaming Frontiers #4, Mar. 2003)
Other Products of InterestD&D v.3.0Legions of Hell (2001) [monsters for Hell in Freeport]
Tree of Life (online resource for Book of the Righteous; 2002) [includes some Freeport references]
Hammer & Helm: A Guidebook to Dwarves (2002) [sample clan in Freeport]
Wrath & Rage: A Guidebook to Orcs & Half-Orcs (2002)
D&D v.3.5Skull & Bones: Swashbuckling Horror in the Golden Age of Piracy (2003; further support by Adamant Entertainment)
The Book of Fiends (2003) [update for Legions of Hell; referenced in other Freeport titles]
The Book of Fiends Web Enhancement (2004)
Codex Arcanis (2005, Paradigm Concepts) [The Arcanis setting includes Freeport and the serpent people. In 2005, a "Living Arcanis" convention event, "Weekend in Freeport," featured four adventures which have not been released commercially.]
Foes of the Fiends (2005)
Stormwrack (2005, Wizards of the Coast) [rules for seafaring campaigns]
D&D 4eLovecraftian Gods (Kobold Quarterly 13, Spring 2010; Open Design)
True20True20 Quick Start Rules (2006) [for Death in Freeport True20]
Call of CthulhuFreeport is heavily influenced by the works of H.P. Lovecraft, other Cthulhu Mythos fiction, and the Call of Cthulhu RPG (1981-present, Chaosium; six editions and myriad supplements). Of most interest to d20 Freeport players would be the Call of Cthulhu Roleplaying Game (AKA d20 Cthulhu; 2002, Wizards of the Coast; further support by Chaosium).
Non-RPG ProductsWalk the Plank (card game, 2007) [for Reading the Skull and Crossbones]
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If I've missed anything or made any mistakes, please let me know, and I'll update the list on my Errata & Notes site here:
http://timsrpgerrata.wikispaces.com/Freeport+Library