|Theories may be removed if ...|
In her youth Cersei Lannister recieved a prophecy from Maggy the frog that she would die at the hands of the "Valonqar", which is the word for "little brother" in High Valyrian. No one person has been confirmed to fill this role; given the circumstances, it could refer to anyone who is a younger sibling.
Tyrion Lannister is the youngest brother of Cersei. Cersei treated Tyrion poorly from shortly after his birth, and suspects him of being the valonqar. Tyrion blames Cersei for Mandon Moore's attempt on his life and for Tyrion's trial.
Jaime is Cersei's twin brother, but was born after her, and is therefore her younger brother. They have shared an incestuous relationship since youth, but drifted apart after Tyrion's trial.
Aegon Targaryen, son of Rhaegar Targaryen and Elia Martell, was the younger brother of Rhaenys Targaryen. Rhaenys and Elia died at hands of Lannister forces. If the person claiming to be Aegon really is Aegon, he has plenty of reasons to want to kill Cersei.
Daenerys Targaryen was the younger sister to her brothers Rhaegar and Viserys and as one of the contenders for the Iron Throne also has plenty of reasons to kill Cersei.
The surviving Stark-children
After the death of their parents and older brother Robb all of the Stark Children (Bran, Sansa, Rickon and Arya) have reasons enough to kill Cercei. Arya has gone as far as to include Cersei on a list of people she wishes to kill.
Stannis is the younger brother of Cersei's former husband, King Robert. He is attempting to overthrow Cersei.
The valonqar passage was a fragment of Maggy's response to Cersei's third question, regarding her, and king's, children. Thus it could be read as "you will see all your children die, and then the youngest will kill you". That would require Tommen to die, rise from dead and only then strange someone to death, like Ser Waymar Royce in the series' prologue.
The Sand Snakes (except Obara)
The Sand Snakes are the daughters of Oberyn Martell and nieces to Elia Martell,both died by the hands of Lannister-men. All Sand Snakes have reasons enough to kill Cercei but because of the circumstance that Obara isn't a younger sibling to anyone she won't fit the prophecy. Her younger sisters Nymeria, Tyene, Sarella or possibly Elia could be candidates, the other three Sand Snakes seem unlikely because of their youth.
Sandor Clegane is the younger brother to his brother Gregor and was for a very long time in service for House Lannister, at least as Joffreys sworn shield and member of the Kingsguard. During the Battle of the Blackwater he deserted and encountered Arya Stark. He travelled together with her through the devastated Riverlands until he was left behind by Arya after he was badly wounded. His fate is unknown till now, a few rumors exist that he is still alive. If he is he could also be the Valonquar because of his despisement for the Lannisters.