Terrible Shotgun: Unique combat shotgun that deals massive damage.
Lincoln's Repeater: Unique BB gun that fires .44 rounds. Found in the American Museum of History in the National Mall.
Xianlong Assault Rifle: Unique Chinese Assault Rifle. Found via the unmarked quest Jigg's Loot.
Alien Blaster: Blaster found next to a crashed alien ship. Very powerful weapon. There is, unfortunately, a very limited supply of ammo for this gun, and it therefore is not a great choice for a standard weapon.
Firelance: An alien blaster aquired via a random encounter. Does slightly less damage than the Alien Blaster, but has the added effect of lighting enemies on fire, adding DPS.
Scoped Gauss Rifle: An energy weapon aquired on completion of the Operation: Anchorage DLC.
Reservists Rifle: Unique Sniper Rifle with a very high critical chance multiplier.
Victory Rifle: Unique Sniper Rifle capable of knocking enemies down for a few seconds upon registering a critical hit.
Blackhawk: Unique Scoped .44 Magnum.
These are just a few of Fallout 3's best weapons. Hope I've been of help to you.