Alphas are the progenitors (or sources) of a certain line of supernatural beings, aka "the original monster(s)." Eve, the Mother of All, is the creator of each line of monster. To create a certain line, she creates a type of infection that changes a human being into that type of monster. She also therefore changes the human's soul causing it to go to Purgatory upon death, rather than Heaven or Hell. According to Crowley and Dean in 7.22 There Will Be Blood all of the Alphas except the Alpha Vampire were killed by Castiel.
According to lore, all Alphas have a connection with their entire race, which allows the Alpha to locate them. For the Alpha Vampire, this connection also allows communication through shared visions or telepathy.
List of Alphas
First appearing in 6.02 Two and a Half Men, this shapeshifter has gathered a following of its offspring and is apparently generating more shapeshifter children by posing as human husbands and impregnating their wives. When Sam and Dean rescue one of its children, the Alpha Shapeshifter storms the Campbell family compound and kills Mark Campbell, overcoming several gunshot wounds and tranquilizer darts, as well as a silver knife to the heart. It then reclaims the baby from Dean and leaves. This shapeshifter is able to transform in just a few seconds without shedding its skin.
At some point this Alpha is captured and taken to Crowley's monster prison. During its interrogation there it takes the form of Crowley's meatsuit. Crowley wounds the Alpha with an iridium knife, and threatens to skin its children in front of it. The Alpha continues to insist that it does not know the location of Purgatory, and seems unconcerned with the fate of its children. Saying that the shapeshifters can make more children. Frustrated, Crowley beheads the Alpha with a machete, killing it.
The Alpha Vampire is first glimpsed in 6.05 Live Free or Twihard, briefly flashing in the minds of its "children" as it commands them to turn more humans recruit more vampires for its army. Nothing is known about this particular monster, aside from the fact its "messages" can be heard telepathically by all vampires and render them unconscious.
In 6.07 Family Matters, Samuel and his people capture the Alpha Vampire and attempt to interrogate him, but he is extremely resistant to pain and does not give Samuel any information. After Samuel leaves the room where he is being held, he is approached by Dean and Sam and he reveals to them that, though he is the first vampire, he has a mother. He also tells them that Samuel is torturing him for information about Purgatory which is where the souls of supernatural creatures go, and where it is located.
Shortly after their conversation, he escapes his cage and almost escapes completely, but demons appear and take him away on Crowley's orders. It is revealed that Samuel has been working for Crowley, who continues to question the Alpha Vampire regarding the location of Purgatory. He is held in Crowley's monster prison, but escapes before Castiel kills every monster inside and becomes the only living Alpha.
The Alpha Vampire makes a deal with the leviathans to share humanity, unaware that they betrayed him he beings panicking when his vampires start dying after eating poisoned humans. He is alerted by Emily to the fact that Sam and Dean are coming for him and captures them. They explain to him that they need his blood for a leviathan-killing weapon and that the leviathans have betrayed him. The Alpha Vampire refuses to believe them until Edgar reveals this to be true and tries to kill him. Sam and Dean dispatch Edgar and out of gratitude, the Alpha Vampire gives them his blood though he promises to "see you next season" which they look forward to.
The Alpha Werewolf is referenced in 6.08 All Dogs Go to Heaven. Crowley speculates that a series of daylight attacks, in which the victim's heart is removed, are werewolf activity and could lead Sam and Dean to the Alpha Werewolf. However, the attacks are actually being committed by a skinwalker.
The Alpha Skinwalker is alluded to in 6.08 All Dogs Go to Heaven. It appears the plan is for a skinwalker pack leader in a town to oversee the recruitment of other skinwalkers in the town, which live with families as the pet dog. On a signal from the pack leader, the skinwalkers will "turn" the families they have been planted with, thus exponentially increasing the recruitment of skinwalkers.
Alpha Khan Worm
The Khan worm was a monster newly created by Eve after she is released from Purgatory, and is therefore the potential progenitor of its species. Although it looks like a cross between a simple slug and a centipede, it is a self-aware, intelligent parasite that can enter a person's ear and take control over their actions as well as access their memories. After it leaves its host's body, a black, gooey substance is deposited in the person's ear.