Federal Courts Jurisdiction Clarification Act of 2006 - Amends the federal judicial code with respect to jurisdictional rules and the amount in controversy in civil litigation concerning: (1) denial of district court original jurisdiction of an action between a citizen of a state and a resident alien domiciled in the same state; (2) citizenship rules for corporations and insurance companies with foreign contacts; (4) removal procedures for civil and criminal actions and summary remand; (5) indexing of the amount in controversy; and (6) the use of declarations to specify damages.