Everyone knows the classic story behind Cubone. It wears the skull of it's dead mother.But Nintendo never talks about HOW Cubone acquires the skull. So, here are just a few of my thoughts.
1: Cubone's mother dies at birth.
The mother Marowak isn't capable of birth, and dies during the process. Simple, but there's a problem. If the Kangaskhan theory is true (Cubone being the baby in a Kangaskhan's pouch) is ever found to be true, this point is made moot. Until then, it seems fully possible.
2: Cubone is violent by nature.
At some point after being born, becoming ambulatory, but before becoming completely cognitive, Cubone enters a state of rage and violence and murders it's mother. As a baby it doesn't realize what it has done, and claims it's skull and enters a deep depression. Eventually, however, the sadness dissipates and after evolving into Marowak, the Pokemon becomes violent again. This one fits in with the Kangaskhan theory moreso, because Cubone would have to be alive for a set period of time before obtaining the skull.
3: Cubone are abandoned at birth
Cubone may not even be raised by their parents at all. It's fully possible that the mother abandons the young Pokemon, and out of spite, the infant uses it's instincts to locate it's parent, kill it, and claim the skull as a method of keeping it's mother close to it. Cubone is classified as the Lonely Pokemon, so, it's possible that it's loneliness stems from being ditched at an early age.
4: Babies are tested for survival.
Going back to Cubone being a naturally violent creature, it's a thought that the Marowak could attempt to condition it's young for life in a trial by combat. If the baby can't kill it's own mother, it isn't fit for survival, and is killed or left to die. If it does defeat the mother, it kills it and takes her skull to wear for it's own protection, to help prolong it's life.
5: The male attempts to kill the child.
Mother Marowak is always the one mentioned, but never the father. It is possible that the male Marowak attempts to kill the baby, perhaps seeing it as a threat to it's patriarchy, and the mother defends it. Both die in the process, and the baby wears the mother's skull out of mourning and respect.
6: A bizarre, fucked up though.
One thing that greatly contradicts Nintendo's suggestion of Cubone wearing it's mother's skull is the fact that when Cubone is hatched, it comes out wearing a skull. This opens the door to a disgusting thought. During the pregnancy, Marowak's skull begins to decay inside of it, slowly killing it until the time the child is born. The creatin from the skull is transfered to the developing baby, forming an outer skull around it's head. The term "mother's skull" implies that it did in fact come from the mother, so it does still fit. This would also partially explain why when Cubone evolves, the skull is firmly attached to Marowak, rather than a helmet style such as Cubone. It also invites speculation to the fact that Cubone never removes it's helmet: maybe it's actually bonded to it's head.