The Ghost Tower of Inverness is located in the Blacks Islands Barony in Aquerra (or at least the crumbling foundation of the ancient tower, the ghost of the tower won't start appearing until I am ready to run that adventure one day).
The town from Against the Cult of the Reptile God, which has the unassuming name of "Hamlet" (pronounced "Ham-lay") in Aquerra, and of course the swamp dungeon as well. (I ran the module in my "The Oath" Campaign)
The Tower of the Heavens which appear ins UK4 - When a Star Falls
Bone Hill (from L1 - The Secret of Bone Hill) - cleared out, but a great site for any up and coming villain to use for nefarious purposes.
The Lost Island of Castanamir from the module of the same name, though the island has since sunk back beneath the waves of the Wilzard's Sea
The Hidden Shrine of the Tamoachan is located amid the Hellish Isles of Aquerra at the fringes of the Empire of Oolam (an expansive Afro-Asian flavored culture built on the ruins of a collapsed Mezo-American Empire of ancient times). This adventure resulted in the TPK of the Oath campaign
Saltmarsh is a town in the Republic of Erthage
Griffon Castle and Capel Tower from N3 - Destiny of Kings and the province of Andevar (now split into East Andevar and West Andevar).
A modified version of Haven from Palace of the Silver Princess
The Caves of Chaos and the Keep on the Borderlands. . . TWICE! The name "caves of chaos" is so generic I thought it would be cool if two different sets of people independently named dangerous caves full of monsters the same thing. In one place (The Far Shore League of western Derome-Delem) the keep is there, but the actual caves are not those from the module. In the Disputed Territories of the Spice & Thread Islands, I used the cave system, but "the Ruined Keep on the Old Borderlands" was exactly that, a ruin that was involved a nearby, but unrelated adventure.
EDIT: This is just the stuff from modules that I can remember. I got a ton of stuff from Dungeon adventures - you should check out the Campaigns page of my Aquerra.wiki (see sig) for more.