Dead Presidents
Scudworth says, "Dead presidents, Mr. B.!" when the X-Blu crew hands him the $2M. This is a phrase used to refer to (US) money, since the portraits on the bills are of past presidents who died a long time ago. Its use is also a bit ironic since there are living clones of the same dead presidents attending the school.
JFK
JFK's dad Wally says, "Baby, a lot of people liked the original JFK because he was such a caring leader, and he inspired a generation of young people." JFK responds, "I thought he was a macho, womanizing stud who conquered the moon!". Both are correct.
Puppet Government
Joan says, "I'm here because I can't stand Abe being Cleo's puppet." A "puppet" government is one that is controlled by some foreign power.
Ancient Pharaohs
Ancient kings of Egypt. Incidentally, Cleopatra was the last Pharaoh. They made pyramids for their burial place, but these pyramids didn't have anything to do with nutrition as Dr. Manson implies.