Naturally Mad Magazine did a parody of all films in the franchise over the years, except for Alien 3. More info here: 
One Gotlib gag has Pépé le Pevert playing the part of the astronaut investigating the strange planet, then having a face hugger alien jump unto his face. However, the creature is so disgusted by it, than he soon lets himself drop and throws up.
Poltergeist: A poster of the film can be seen hanging in Rob's room.
The chest burster scene in Space Balls has John Hurt reprising his role, shouting No, not again! in the process. The little alien then hops out and does a little sing-and-dance routine, parodying the Michigan J. Frog in One Froggy Evening.
In another episode where the Warners crash a celebrity party, they meets Sigourney Weaver and a xenomorph. Dot introduces it to one of her "pet" monsters inside her box, this time the Director with a talking tongue.
Tongue: Oh monster!
American Dad!: In Great Space Roaster the way the Smiths wake up in the pods, and Stan's panties and tank top outfit are the same as Sigourney Weaver's in the end of Alien. The way Roger acts while hunting down the family on the spaceship is exactly like Alien.