Before you set out and begin murdering every sentient and vaguely helpful creature in Drangleic, there are some things you should know as, outside of the moral quandries you might face when killing people you might have grown attached to, there are several consequences. First and foremost, although it should be obvious, you are going to be KILLING them so make absolutely SURE you are DONE with them. They'll be alive once again in the next cycle, but until your dark work is complete you may find yourself inconvenienced if you discover you forgot to buy out a stock of effigies or herbs or whatever you might need. Secondly, if you are in a covenant like Blue Sentinels or Brotherhood of Blood, you WILL be ejected upon attacking your covenant leader.

Lastly, and most importantly, is sin. Every NPC you kill will increase your sin counter by 1. This sin CANNOT be absolved by the Pardoner, and neither can it be removed by beginning NG+. By the time you're through, your sin counter will bei n the high 20s/low 30s, which WILL designate you a "Sinner" on your character sheet and make you a target for Blue Sentinels using Cracked Blue Eye Orbs. Every time they kill you, your sin count will decrease by 1, which will continue until you have less than 10 sin. In short:

Killing an NPC = +1 sin
Being killed by a Blue Sentinel Arbiter spirit = -1 sin
Blue Sentinel invasion range = >= 10 sin

As Majula is the hub of the game, the vast majority of the NPCs you need to kill are here, including:

The Emerald Herald - Drops an Aged Feather if you somehow didn't get it from her in the Dragon Aerie
Lenigrast the Blacksmith - Drops a Blacksmith Hammer, even if you already got one
Chloanne the Stone Trader - Drops some infusion materials
Cartographer Cale - Drops his helm, even if he already gave it to you for beating all major bosses
Armourer Maughlin - Drops his armour set
Laddersmith Gilligan - Drops a Miniature Ladder and a Melu Scimitar.
Licia, the False Priestess - Should be killed with the Crushed Eye Orb, but drops a miracle, her armour set, the key for the nearby contraption, and a chime.
Carhillion, the Mage - Drops a Nothern Ritual Band +1
Rosabeth, the Pyromancer - Drops a Fire Seed
Saulden, the Crestfallen Warrior - Drops a Ring of Steel Protection +1, even if he already gave you one
Melentia, the Merchant Hag - Drops a Covetous Silver Serpent Ring +1.

Sweet Chalquoir is invincible, and cannot be harmed in any way.

Collector's note - kill Melentia last, as she will sell the armour sets of most NPCs you kill, including sets that are otherwise nearly impossible to get like the Brotherhood of Blood armour set.

Some NPCs have longer questlines, and their items can be acquired either completing their stories, or by killing them. The two options are mutually exclusive, as the NPCs will disappear from your game once you get your reward. Completing their questlines is greatly preferable, as you will get ALL of their items as opposed to only a few. Such NPCs include

Mild-Mannered Pate - Located in either Forest of Fallen Giants, Earthen Peak, or Brightstone Cove Tseldora. Drops his spear and ring.
Creighton - Located in Huntsman's Copse, Shaded Woods, or Brightstone Cove Tseldora. Drops his helmet.
Lucatiel of Mirrah - Located in No-Man's Wharf, Earthen Peak, Lost Bastille, Black Gulch, and Aldia's Keep. Drops her mask.
Benhart - Located between Shaded Woods and Majula, Drangleic Castle, Forest of Fallen Giants, and Memory of Orro. Drops the Bluemoon Sword.

As already noted, attacking the leader of a covenant you currently a member of WILL kick you out. You will not lose any progress and can rejoin in NG+ or, should you have the patience of a saint, wait until the gravestone appears. This can take several hours.

The Rat King - Either in Grave of Saints or the Doors of Pharros, behind the respective boss rooms. Drops nothing; regicide is its own reward.
Targray, of the Blue Sentinels - In the Cathedral of Blue, behind where you fought Dragonslayer Ornstein. Drops his halberd.
Tiny Gren, of the Brotherhood of Blood - In the Undead Purgatory, behind where you fought the Executioner's Chariot. Drops his hood.
The Belfry Puppets, the Bell Keepers - In either Belfry Sol or Belfry Luna. Drops a Rusted Coin. Their lives are bound, and killing one will kill the other. Belfry Sol's is easier to kill, as you cannot be invaded while in his room.
Treasure Hunter Magerold, of the Dragon Remnants - In Iron Keep, in a side corridor near the front entrance. Drops a Gold Covetous Serpent Ring +1.
Darkdiver Grandahl, of the Pilgrims of Dark - In the foundations of Drangleic Castle, Black Gulch, and Shaded Woods. Drops his Dragon Chime.

Milibeth the Handmaiden - Drops 3 human effigies
Strowen, the Narrator - Drops 6 human effigies
The Other Two - Drop nothing.

Sorceror Straid - In Lost Bastille. Drops his hood.
Ornifex, the Servant of Velka - In Shaded Woods, or her house in Brighstone Cove Tseldora. Drops nothing.

Cromwell, the Pardoner - Located in Brighstone Cove Tseldora. Drops a Ring of Resistance.
Gavlan, Wheeler and Dealer Extrordinaire - Located in No-Man's Wharf, Harvest Valley, and the Doors of Pharros. Drops a Gyrm Greataxe.
McDuff, the Blacksmith - Located in Lost Bastille. Drops a Titanite Slab, even if you already got his.
Manscorpion Tark - Located in Shaded Woods. Drops a Second Dragon Ring.
Felkin, the Hexer - Located in Huntsman's Copse. Drops his Sunset Staff.
Head of Vengarl - Located in Shaded Woods. Drops his helmet.
Captain Drummond - Located in Memory of Vannar. Drops his helmet.
Navlaan and Navlaan - Located in Aldia's Keep. Drops his hood.
Agdayne, the Grave Warden - Located in Undead Crypt. Drops his kilt.

Royal Chancellor Wellager is a ghost and cannot be harmed. Odd, that.

Congratulations, you've now murdered everybody of note in cold blood. If you haven't seen them already, the Blue Sentinels are now out for your head, so try to take at least a few of them down with you. Good luck with New Game Plus!