>Strong Bad has yet to appear yet...
>>else start out as an honest-to-badness bad guy?

Uh, Strong Bad isn't a real person.

Gryphon, Zoner, Truss, and the rest of the WPI people started off as good guys, Redneck and Doc Mui and Marty Rose all did as well. Anne Cross was a fugitive, but from the Psi-Corps, so that doesn't really count. Jedi Anne definately is a good guy. Janice is as well. Geoff is the only real person I can think of who wasn't on the side of right, and is a criminal by the standards of Gryphon (or at least, by the standards of law that Gryphon established) and all the rest, as well, on his introduction.