Throughout the world you will see Pharros' Contraptions that look like a stone face on a wall or floor. If you insert a Pharros' Lockstone into the contraption, you will trigger an event that can be either a secret or a trap. Here are four contraptions you should make sure to seek out.
Forest of Fallen Giants (Cardinal Tower): Head down the ladder in the back of the ballista room to find a illusory wall contraption that yields a Titanite Slab and the Chloranthy Ring.
The Lost Bastille (Servant's Quarters): In the outdoor area with the well and dogs there will be a room with a raised platform in it. Entering through the windows is the easiest way to get on the platform and you can turn right to find an illusory wall contraption that opens two areas. One of the areas has a Soul Vessel, while the other has a cage elevator and a Wilted Dusk Herb.
Undead Crypt (Undead Ditch): After the shield-wielding Imperious Knights, drop down the hole and head straight ahead and slightly to the left to the wall in front of you (there is no stone baseboard in this region). Press the action button on the wall to open it and there will be an illusory wall contraption in front of you. The wall that it illuminates is directly opposite your current location and there is a Great Lightning Spear inside.
Dragon Shrine (Shrine Entrance): Head up the stairs and kill the Drakekeeper. The illusory wall contraption is located just behind him under the stairs. It opens the wall to the left containing the Staff of Wisdom and the Judgment armor set.
Can be used to reallocate stats by giving one to the middle of the old firekeepers in Things Betwixt. (Note: You cannot lower a stat below the original base stat of your class.)
Majula: Obtain the Mansion key from Cale the Cartographer (located in a cave in the large open area after the first fog gate) and defeat the skeleton in the basement. In the back left corner of the basement you will find a chest that contains the soul vessel. If it is not a soul vessel, closing the game and restarting it will allow you to open the chest again.
Using a bonfire ascetic on the Majula bonfire does not grant you another soul vessel.
Majula: Speak with Crestfallen Saulden (sitting next to the obelisk) after bringing 4 NPCs to Majula and he will give you a soul vessel.
The Lost Bastille (Exile Holding Cells bonfire): In the area just before Steady Hand McDuff's workshop (contains 2 dogs and an Undead Jailor) there is a boarded up entrance that you can destroy. Open the door with the Antiquated key, or hit it with a weapon. This will cause the Royal Swordsman on the other side to open the door. Straight ahead will be a building with a raised platform in the back. Once up on the platform, turn left down a passageway and use a Pharros' Lockstone to open two secret rooms. The closer room contains a chest with a soul vessel in it.
This soul vessel respawns when you use a bonfire ascetic on the Exile Holding Cells bonfire.
Drangleic Castle (Central Castle Drangleic bonfire): Kill an enemy near the golem up the ladder to bring it back to life and activate the elevator. Ride the elevator up to the top and the soul vessel will be in the middle chest.
You do not have to enter the room with the golem. If you have magic and the binoculars, you can open the gated door and kill the last stone soldier on the left. This will activate the golem and you can head back down the ladder.
Undead Crypt (Undead Crypt Entrance bonfire): Just before the fog gate, if you drop off the edge to the left, you can enter a room containing a chest with the soul vessel and a ladder to get to the next bonfire.
Memory of Orro (Giant Tree on the ramparts in Forest of Fallen Giants): At the start take the right doorway and turn right immediately in the room where Giants are fighting soldiers. You will see a corpse in the corner with the soul vessel.
This soul vessel respawns when you use a bonfire ascetic on The Place Unbeknownst bonfire, but in order to do this you must defeat the Giant Lord boss.