In appellate cases, the party appealing is called the "petitioner", and the other party is called the "respondent". These cases are listed Petitioner v. Respondent.
In your example, Twombly was the original plaintiff, and Bell was the defendant in a class-action. This initial action would have been referred to as Twombly v. Bell. The case was dismissed by the trial court.
Twombly appealed to the 2nd Circuit Court of Appeals. This action would have been still been called Twombly v. Bell, since Twombly was the party petitioning for the appeal. The 2nd Circuit agreed with Twombly, and reversed the district court's decision.
Bell, then on the losing side, decided to appeal to the US Supreme Court. Because Bell was the petitioner in this action, Bell gets listed first.