Perks

Each survivor can gain up to 3 perks by training skills (at levels 4, 7, and 10 I believe, after you talk to them and learn more of their backstory), and more through other means. Some survivors arrive already with perks (note however that none of them arrive with their "training" perks already taken, you can always "talk" to them 3 times, each time gaining a perk). Some perks are given by random events (permanently, in most cases, or, in rarer cases such as becoming an addict or a cultist, until countered) or provided by items (for as long as those items remain equipped). Perks provide various bonuses (and sometimes penalties), such as additional skill points or increased effectiveness with certain missions. The main leader has a special perk chosen at the start of the game which affects the entire fort, does not gain perks from training, but is (or at least was in earlier versions) still eligible for all event-based perks (doesn't seem to work for me lately, need confirmation).

There does not seem to be a limit to the number of perks any survivor can have.

Main Leader Perks

College Student	+science, schools and bars are 25% more effective
Construction Worker	+building, -50% material costs for building
Doctor	+science and -1 day injury recovery time (Note: it is used in a number of events either enabling more options, or outright changing the outcome)
Gang Member	+2 Defense, no happiness loss from death or injury
Hobo	+2 Scavenging, +5 housing space
Police Officer	+2 Defense and +1 bonus on firearms for all survivors (eg: +3 Shotgun becomes +4)
Politician	+2 Leadership and one bonus starting survivor
Priest	+2 Leadership, church, more devout survivors
Retiree	+2 building and +10% happiness bonus
Shop Clerk	+scavenging and +25% trade bonus (Note: The bonus is purely additive, I.E. a 15% mark-up becomes a 10% discount)

Deluxe Jobs

Your main character can only acquire these perks if you, as the customer, purchased the Deluxe Edition of Rebuild 3 ($25 from the RebuildGame.com website). If you only purchased the normal edition ($15), then these perks are not available to you.

Pizza Delivery Driver	+scavenging, start with Driver perk
Pro Gamer	+defense, higher base defense but increased danger all-around
Programmer	+3 Engineering, start with a lab and 9 researched tech (Note: the research is always the same: top tier walls, top tier survivor attracting, plus all their prereqs, however if the story mode locks the tech level you will gain less than 9 techs)
Real Estate Developer	+3 Building, all build missions take 1 day
Rock Star	+3 Leadership, gain respect x2 faster, lose respect x2 slower

Skill-related Perks

Leadership

Born Leader	+3 Leadership skill
Musician	Bonus happiness to others during missions (Note: this is also a randomly "triggered" bonus)
Negotiator	Bonuses while trading with factions (Note: Triggers all the time, but requires the faction to have at least one unit of food or materials or fuel left in their stock, the ones that you trade them do not count for that purpose)
Preacher	More effective while working in a church
Peacekeeper	Reduces chances of riots and fights

Defense

Fighter	+3 Defense skill
Firearms Training	+1 Defense with anything from pistols to machine guns
Melee Training	+1 Defense with anything from a shovel to a sword (wasn't it +2? please, confirm(never was it +2))
Hand to Hand Combat	+2 Defense when no weapon equipped
Demolitions	Explosives do extra damage
Commander	All survivors gain +0.5 to defense

Building

Handyman	+3 Building skill
Artist	Happiness bonus when fortifying buildings
Redecorator	May automatically convert useless buildings (Note: This means that very infrequently, the survivor will trigger a random event to instantly convert a useless building in your fortress like an XXor Gas to a building that serves a purpose (I.e.Farm). It does not improve any of the missions that you assign the survivor to. Also, keep in mind that some "useless" buildings can still have event uses. For example XXor gas can be used in last judgement event, and 8-12 mart can be used in "Ice cream" event)
Tools Expert	Double skill bonus from tools (seems to apply only to Building bonuses)
Defenses Expert	Grant +1 defense to all buildings

Scavenging

Resourceful	+3 Scavenging skill
Good Cook	Bonus food production (Note: This means that on rare occasion, this survivor will trigger an event that instantly creates extra food out of nothing.)
Green Thumb	Bonus food while farming (Note: this is also a randomly "triggered" bonus) Also obtained when equipped with Pitchfork or Pea Gun
Hoarder	Extra building materials while scavenging (Note: this is also a randomly "triggered" bonus)
Scrapper	Scavenging skill is also added to defense

Engineering

Genius	+3 Engineering skill
Bookworm	Research bursts, double Engineering from books (Note: "Research Bursts" means that if this survivor is working in a Laboratory, then there is a chance that the current research project will abruptly finish early.)
Crafter	Creates extra items in the workshop (note: the items created are free, IE making extra traps doesn't cost extra materials)
First Aid	Reduces chance of death on missions
MacGyver	Half of Engineering skill added to defense.

Positive Perks

Animal Lover	Extra skills and happiness if equipped with a pet. +1 Defense, Leadership. Overridden by Allergic to Pets.
Camper	Sleeps under the stars, does not need a house
Driver	Does missions faster when equipped with a vehicle (this is also a randomly triggered bonus)
Easy Going	Double happiness increases and halve decreases
Fast Recovery	Recovers from injury faster
Fearless Reclaim	Can reclaim buildings with zombies on them. (Note: This does not allow the builder to ignore Zombie Mobs or Massed Zombies. Those problems must be cleared out of the way, first. Nor can the builder reclaim an unscouted tile.)
Half Rations	Eats less than other survivors
Hunter	Improves hunting missions. learn-able and given by hunting rifles, crossbows and Melanie's boomerang
Immune	Won't die from a zombie bite, +1 defense.
Loner	Improved skills when on a mission alone. (It means he/she will do better if doing a mission alone. Ex: A loner with 5 defence skill killing zombies alone will seem to have a defence skill of 7(Not accurate, It's only an example))
Musician	Bonus happiness to others during missions (Note: this is also a randomly "triggered" bonus)
Ninja	No penalty for how far away a mission is. (Some weapons, such as named swords, also add this)
Scholar	Learns more from schools (note: "more" means faster, nothing more)
Superhero	Increase each skill by 1. Increase max levels by 1. (Technically speaking this skill does NOT increase skill maximum. You keep the same "natural maximum" of 10 in each skill, and just gain a +1 bonus to each skill on top of what your "natural" skill level is. Each survivor can train up to 10 skill levels in each "class" and can only get above that with various bonuses such us equipment or perks. For example with fighter perk (and no other skill modifiers) a fully trained survivor would have 13/10/10/10/10 while with this perk (and no other modifiers) it would be 11/11/11/11/11)
Team Player	Improved skills when on a mission with at least 3 survivors (a specific Gaming Book will also add this)

Tradeoff Perks

Addict	Regular user of the drug Bath Salts, +1 Defense.
Brave	+1 defense, but may take the hit for another survivor.
Coward	Less likely to be injured, but -2 leadership
Cultist	Follower of The Chosen Ones, +10 Happiness (Note: Cultists on Kill Zombies missions have a random chance to abandon their mission, lose happiness, and take mandatory time off because killing zombies goes against their religion. Anyone stacked with a Cultist is likely to become a Cultist.)
Devout	Extra happiness from churches, none from bars.
Eccentric	Makes both friends and enemies easily.
Intense Focus	-1 to all skills, but learns faster in missions.
Light Sleeper	+0.5 to all building defense, but happiness increases at half the normal rate.
Pacifist	Factions like you more, but no bonus from weapons. (Will still gain bonus from nonweapons)
Skeptic	+1 engineering, immune to religion (Will not be a devout or a cultist. Won't gain happiness from preachers. Devouts and cultists will not gain this perk)
Stinky	+1 defense, but hard to make friends.
Tough	Less likely to die, but hard to make friends.

Negative Perks

Allergic to Pets	No benefit from equipping animals. Overrides Animal Lover.
Clumsy	Increased mission danger
Double Rations	Eats more than other survivors.
Downer	Lowers happiness of other survivors when on missions.
Rebellious	May refuse to work. (Note: Will cause the survivor with the perk to have a random chance to abandon their mission and take mandatory time off.)
Sickly	More likely to get sick

Item-Based Perks

Caretaker	Periodic Increases to Happiness, granted by any child (kid or baby). (Confirmed this is a periodic increase and not a flat 10%)
Defended	Prevents death on missions. Granted by the Helmet. (Lost after one use along with the helmet)
Pet Owner	Periodic Increases to Happiness, granted by any pet (dog or cat). (Confirmed this is a periodic increase and not a flat 10%)
See Further	When scouting, scouts adjacent (not diagonal) buildings as well in the same time, very effective with larger tiles. Granted by named binoculars. (Simple "Binoculars" only grant the universal +1 to scavenging"
Vehicle	Removes mission danger caused by distance from fort. Granted by Bicycle, Motorbike, Car, and Armored Car.

Faction Perks

Former 1337cREw	Increases sway with the 1337cREw faction
Former Chosen One	Increases sway with the Chosen Ones faction
Former DAHLIA	Increases sway with the Dahlias faction
Former Luddie	Increases sway with the Luddies faction
Former Pharmacist	Increases sway with the Pharmacists faction
Former Pig Farmer	Increases sway with the Pig Farmers faction
Former Riff	Increases sway with the Riffs faction
Friend of Gustav	Increases sway with Gustav the trader
Government Defector	Increases sway with the Government faction
Last Judgement Escapee	Increases sway with the Last Judgement faction
Rotten	Increases sway with the Rotten faction
St. Michael's Dropout	Increases sway with the St. Michael's Boys faction

Leader Bonus Perks

After certain events, your leader can pick a bonus perk. No items are given with these perks.

In Wenatchee, if you choose to "safely rescue as many kids" in the farm disaster quest line (Starts after the CDC research is obtained; one observation was 10 days after, another says 30 days after), then Meet with Ludd, then wait about a day or two, you can pick from (couldn't obtain the perk in Iphone version, need to be confirm)

Police Officer
Gang Member
Rockstar (Deluxe)

In Moses Lake, if you agree to let one of them use the mall, then choose to "Let them kill one another" in the Gangs of Deadsville quest line, regardless of which side you favor, you can pick from

Politician
Priest
Pizza Delivery Driver (Deluxe)

In Spokane, if you choose to defeat the Government with Jesse, you can pick from - In later patches: If you side with Davis and capture rotten faction members for the government, you can pick from

In Nelson, after completing the Ice cream truck quest line, you can pick from - In later patches: If you choose to keep the pig farmers' secret at the end of the questline, you can pick from

In Kelowna, if you choose to take down the Last Judgement with the Dahilas, or choose to sneak Mason Moon and the girl out of the city, you can pick from

Chilliwack, after completing the Riffs quest line, you can pick from