There have been maybe one or two "Indiana Jones" references and one "Back to the Future" reference, but nothing presented as a special. Other movies that I would like to see "Family Guy" parody are: (think of your idealistic casts)
"The Wizard of Oz"
"Alice in Wonderland"
"The Matrix"
"Teenage Mutant Ninja Turtles"
"Ghost Busters"
"The Addams Family" or "The Munsters" (they have done "Brady Bunch" references)
"Titanic" (the original story, not the corny Leonardo DiCaprio and Kate Winslet version)
(Several horror movies - "Night of the Living Dead", "Halloween", "Friday the 13th" (wait, they have done references, never mind), "a Nightmare on Elm Street", "Dracula", "Frankenstein", "Child's Play", "Christine", "the Fly", "the Blob", "the Exorcist", etc. mostly the popular and well-likable ones)
Possible T.V. show parodies:
"Spongebob Squarepants"
"Silly Symphonies" or "Looney Tunes"
Possible video game parodies:
"The Legend of Zelda"
"Super Mario Bros."
"Mega Man"
There are probably many more, but I will think of more later, enjoy.
Looneytunes/Disneytoons