Fallout 3 weapons

Pistols

 * Unique weapons are highlighted with a darker background.
 * Pistols are affected by Gunslinger.
 * ¹ Weapon is silenced.
 * ² Weapon is scoped.

Rifles

 * Unique weapons are highlighted with a darker background.
 * Rifles are affected by Commando.
 * ¹ Weapon is silenced.
 * ² Weapon is scoped.

Shotguns

 * Unique weapons are highlighted with a darker background.
 * Sawed-off shotguns are affected by Gunslinger.
 * All other shotguns are affected by Commando.

Submachine guns

 * Unique weapons are highlighted with a darker background.
 * SMGs are affected by Gunslinger.

Direct-Fire

 * Unique weapons are highlighted with a darker background.

Area-of-Effect

 * Unique weapons are highlighted with a darker background.
 * Area-of-Effect weapons have a Crit % Modifier of 0, which eliminates any chance to critically hit with them.

Energy pistols

 * Unique weapons are highlighted with a darker background.
 * Energy pistols are affected by the Gunslinger perk.

Energy rifles

 * Unique weapons are highlighted with a darker background.
 * All energy rifles except the Tesla cannon are affected by the Commando perk.

Bladed

 * Unique weapons are highlighted with a darker background.
 * Melee damage is doubled in V.A.T.S.

Blunt

 * Unique weapons are highlighted with a darker background.
 * Melee damage is doubled in V.A.T.S.

Unarmed

 * Unique weapons are highlighted with a darker background.
 * Unarmed damage is doubled in V.A.T.S.

Custom-built weapons

 * Red codes are for the Schematics.
 * Cryolator, also a custom-built weapon, was cut from the game

Cut content/Not in game

 * Unique weapons are highlighted with a darker background.
 * Melee and Unarmed damage are doubled in V.A.T.S.

Concept art weapons
These weapons were made into concept art but never made into the base Fallout 3:
 * Cryolator
 * Mason jar mine
 * Piggy bank grenade
 * Air hammer gun