eCos: here are the ones that comes to my mind right now:
persuasion/intimidation/axii sign hex: gained and improved by using them in dialogue.
assasin: gained when u find the Assasin's Creed easter egg in the Ballista quest during prologue. (there is a corpse of a white hooded man with a red sash near the ballista). also heard this may be gained by attacking a foe from behind while he is occupied with another.
conjurer: i'm not sure exactly but one way is to use axii during dialogue, another is to use more than one sign to defeat a foe i think.
strong back: carrying Aryan LaValette to the exit during the escape from the dungeons. also heard you may gain it if you escape from dungeons overencumbered, but that's not %100 sure.
cover: by staying inside Triss' shield spell, at the beginning of chapter 1.
strong stomach: after the completion of Hung Over! quest
thrower: beating Ves in knife throwing in Blue Stripes' party.
exorcist: not sure but by either freeing Henselt of the blood curse, or completely ending it
exterminator: not sure about this one, may be imagining it :) but gained by completing a certain number of contracts i think
also heard there are a pyromaniac and haggler perk but don't know how to get them. using igni at a special time for the former i guess.
pretty sure i missed some, but that's all i can think of right now.
You do not gain Assassin through backstabbing foes, you can't get Conjurer through using signs in combat, and you can't get Strong Back through getting overloaded. The
only way to get these abilities is to find the Assassin's Creed Easter egg, use Axii in dialogue, and carry Aryan through the dungeons. You get Strong Stomach through using the special potion during the Kayran quest, not through the Hung Over! quest. You get Pyromaniac through taking a specific amount of damage via being incinerated - you can do this through stepping on fires over and over again.
There are a total of thirty Abilities in the game files, though only Axii Sign Hex, Persuasion, and Intimidate have any extra levels (each has three). All the others have a single level.
I'll put up a list of all thirty ability names (translated from Polish, as that's what's given in the game files and we don't have access to the English text files yet) and their effects in a bit.