Fallout 3 secret weapons

If you mean unique weapons here are some:

A3-21's plasma rifle. - upgraded version of the plasma rifle
Fat man- Experimental MRIV is the upgraded unique version
Alien blaster- Firelance is the upgraded version
Fawks super sledge - upgraded version of the super sledge
Smugglers end - Upgraded lazer pistol
Wazer wifle - upgraded lazer rifle
Lincolns repeater rifle - Upgraded hunting rifle
Xaulong assult rifle - upgraded assult rifle

All these are unique varients of the normal versions that do more damage, are worth more and are just overall better.