The quote "I heard that the dolphins are doing a good job contacting the extraterrestrials. I heard that from the mice!" from Orthopox is a reference to "The Hitchhiker's Guide to the Galaxy" (radio series, books, TV series, album, movie, towel, etc).
All the members of the Furon Race are all named after diseases and viruses on earth - Cryptosporidium (for Crypto), Orthopox (for Pox), and Menengitis, for example.
The gas-mask worn by Silhouette is the mask from the Pandemic Studies logo
The character of General Armquist is satirizing real-life General Douglas MacArthur, who also has a signature corn-cob pipe.