There's a rather long-winded piece of dialogue which ended up referencing, of all things, the song "My Girlfriend Who Lives In Canada" from Avenue Q, even going as far to mention that said girlfriend is a lie.
Also, how many Alices it would take to make her useless? 42. And Agent X.
Manfredi and Johnson, the two characters Skipper mentions on occassion, are the names of the prisoners killed in the opening of Stalag 17.
"Lemur See, Lemur Do" starts with Julien finding a crate in a way closely resembling some apes finding The Monolith. There's even the music.
Skipper(looking into viewfinder): "I got my eye on some kid and his beagle in a pumpkin patch. What a blockhead."
To their own Christmas Caper special in "Hello, Dollface". Some guy picks up Private and squeezes him like the crazy lady, Private poots like in the special and the dude says, "A talking penguin? What is this, 2005?" 2005 being the year that short was made.