The names of many unique weapons are clear references:
•"Occam's Razor" is a reference to the scientific principle of the same name.
•The "Board of Education" is a reference to the paddles once used for corporal punishment, as well as the government body that oversees schools in a specific area.
•A Ripper called "Jack" is a reference to Jack the Ripper.
•A metal saw called the "Man Opener" is a play on "can opener".
•A pool cue called "The Break" is a reference to the Pool term of the same name.

The Wanamingo from Fallout 2 was at one point planned to be in the game, but was never added into the final version. Concept art shows it as a possible variant of the original, being much bigger and without tentacles.

Concept art and unused models exist for cut weapons referred to as the "Kryolator" and "Kryo-Grenade." While the grenade itself made it into the Mothership Zeta DLC with a new texture and mesh, the "Kryolator" was ultimately cut in the final version of the game, existing as only a mesh with textures. However it did later appear as a usable weapon in Fallout 4.

Concept art was produced showing that there was a possible third size-class for the Super Mutants, labelled as a "Spinebreaker." In terms of size, the Super Mutant Spinebreaker would have been somewhere between the regular Super Mutant Grunts and Super Mutant Behemoths, effectively being the second size class of Super Mutants.

In the Broken Steel DLC, in the cutscene used for when the player character travels on the Presidential metro, the moving train is not a separate entity programmed to move on its own due to limitations with the Gamebryo engine. Instead, when the player goes on the metro, a script is triggered that equips an NPC underneath the train with a glove that turns its right hand invisible and produces the model for the Presidential metro car on top of it appearing like a giant hat. This then triggers an animation of the NPC's model sitting down and gliding along the ground in an arc that simulates the metro riding along the subway tracks.

Rivet City's Abraham Washington is the name of this NPC and is a reference to two former United States Presidents, George Washington and Abraham Lincoln.

An unused set of Enclave Power Armor can be found in the game files and spawned in-game, utilizing console commands.

The stats differ and the armor set carries the file name, "Robo-Thor Armor", evidently a reference to Marvel Comic's Thor, as the armor helmet has a unique design reflective of Thor's own signature helmet.

According to former character artist Jonah Lobe, the response from Fallout fans and the fan website "No Mutants Allowed" to Bethesda purchasing the series from Interplay Entertainment and developing Fallout 3 consisted of "a lot of excitement, a lot of enthusiasm, and a lot of death threats." Lobe claimed that while he and other employees at Bethesda were not "privy" to most of the details on the threats due to the company shielding them from its workforce, as a result of the overwhelmingly vocal and mixed responses from fans, Bethesda had to hire a security guard for the first time in its 21-year history.