I tried to only use characters who are "currently alive", or were the last time we "saw" them. For instance, my initial choice for Secretary of Defense was John Winchester, and the Secretary of Health and Human Services was Betty Ross. Oops. Also, several characters switched jobs. For instance, Karl Agathon, now a member of the Secret Service, was my initial choice for Vice President before I figured out that Mitchell Hundred would be better suited for the job. Ororo Munroe was my original EPA pick before Benjamin Linus came to mind. Anyway, you get the idea. Here we go.
President - Leland Joseph "Lee" Adama
Vice President - Mitchell Hundred
Secretary of State - General George S. Hammond
Secretary of Defense - Scott Summers
Secretary of Education - Professor Minerva McGonagall
Director of National Intelligence - Colonel Nicholas Joseph "Nick" Fury
Secretary of Transportation - Kurt Wagner
Secretary of the Treasury - Warren Worthington III
Secretary of Housing and Urban Development - Forge
Homeland Security - Colonel Saul Tigh
Secretary of Health and Human Services - Doctor Henry McCoy
EPA Admin - Benjamin Linus
Secret Service - Nathan Summers, Wade Wilson, Bruce Wayne, Wally West, Bucky Barnes, Natalia Romanov, Clint Barton, Matt Murdock, Worf, Teal'c, Ka D'Argo, Bill Compton, Varlyn Stroud, Dean Winchester, James Proudstar, Odo, Jayne Cobb, Richard Alpert, Sayid Jarrah, Mabius, Danny Rand, Luke Cage, Pietro Maximoff, Benjamin J. Grimm, Kara Thrace, Rick Deckard, Karl C. Agathon