Fallout 3 Perks

General information
In Fallout 3, you will gain a perk every level (as opposed to every three levels in Fallout and Fallout 2, and every two in Fallout: New Vegas).

There are :
 * 59 regular perks, 5 special perks and 7 quest perks in the normal game
 * 1 special perk in Operation: Anchorage
 * 1 special perk and 2 quest perks in The Pitt
 * 14 regular perks in Broken Steel
 * 1 special perk, 2 quest perks and 3 cut perks (impossible to get without using the console) in Point Lookout
 * 1 special perk in Mothership Zeta

Also, unlike previous games, traits that gave you both bonuses and penalties at the same time are no longer in the game. Instead, some of them (like Bloody Mess) were changed into perks.

In Fallout 3 a perk's S.P.E.C.I.A.L. requirements cannot be met by equipping items or using drugs (with the exception of the Lucky 8 Ball).

Special perks
You can get these perks by special actions or interactions with other characters.

Important note about special perk codes: Trying to add them before doing the special actions or interactions with other characters may cause game to crash or corrupt.

Quest perks
You can get these perks as a reward for quests.

Important note about quest perk codes: Trying to add them before doing the quest required may cause game to crash or corrupt.

I'm not sure if the "hidden perk" is considered as a perk because it doesn't appear as a perk in the pipboy, in any case you will get 10 DR after you completed the option part to cripple yourself in the wasteland survival guide.

Add-on perks
Perks available through add-ons.

Regular perks
These perks are added only in Broken Steel.