Toy Story/Shout Out

Series wide

 * The "Pizza Planet" truck has showed up in almost every Pixar-created work.
 * Each movie in the trilogy contains a shout out to its corresponding film in the original Star Wars trilogy:
 * Toy Story: Buzz talking about delivering secret plans that reveal the weakness of a weapon that can destroy a planet, and Sid's "Where's the rebel base? Talk!" (A New Hope)
 * Toy Story 2: Zurg's "I am your father", plus the Big No from that follows. (The Empire Strikes Back)
 * Toy Story 3: Big Baby (Return of the Jedi)
 * The overall plot and tone of the series (especially the third film) has more than a glancing similarity to The Brave Little Toaster -- the first feature-length film Lasseter and Ranft worked on.

Toy Story

 * When Woody is holding the staff meeting before Sarge and his men are sent out, there's a book on the shelf behind Woody called "Tin Toy". It's a thin green one.
 * The little binocular wind-up toy could be a reference to the same character appearing way back in the cute Disney documentary Where The Toys Come From.
 * The titles of several Pixar Shorts appear on books on Andy's shelf.
 * Perpetually-anxious Rex spouts "I just don't think I can take that kind of rejection!" then later "I don't like confrontation!", two lines from perpetually-anxious George McFly.
 * After calling Woody "a sad, strange little man", Buzz does the Vulcan salute.
 * Pizza Planet's entrance is guarded by old-school Cylon centurions. Behold!
 * Both the Alien Slime soda dispenser and the Whack-a-Alien game at Pizza Planet are a reference to the titular monster from the film Alien.
 * When Buzz (excuse me, "Mrs. Nesbitt") is having tea, he says he's "sucking down darjeeling with Marie Antoinette and her little sister." The dolls are both headless, so which is which doesn't matter so much, but this is (potentially) referencing both Marie Antoinette's fate of beheading and Wednesday Addams's doll.
 * While trying to escape Sid's house Woody repeatedly calls out, "There's no place like home!".
 * Woody's head spinning all the way around.
 * Big Baby doing the same in the third movie.
 * In the chase scene at the end, you get a quick glance inside the car, and the radio's playing Hakuna Matata.

Toy Story 2

 * In the opening sequence, listen close and you'll catch at least half a dozen classic sound effects from Star Wars, including the Darth Vader breathing, the lightsaber sound, and the blaster sounds from both the X-Wing and TIE Fighter.
 * And the Luke, I Am Your Father moment between Zurg and Buzz.
 * Pay close attention as they flip through the channels and you'll see snippets from several Pixar Shorts on the TV.
 * The toy repairman is Geri from the Pixar Shorts Geri's Game, where he plays a game of chess against himself. While he's repairing Woody the music from the short plays and one of the drawers in his toolbox is filled with chess pieces.
 * Rex with "Objects are closer than they appear" in the toy car's rearview mirror in Toy Story 2, to the scene DEAD ON from the T-Rex Chase in Jurassic Park, Hilarity Ensues.
 * Potato Head takes off his hat and throws it at the door of Al's apartment building to keep it from closing. Oddjob from Goldfinger couldn't have done it better.
 * There are A Bugs Life toys in Al's Toy Barn.
 * Buzz comes across the new line of Buzzes in the toy store, and notes the snazzy utility belt, saying "I'd like to get me one of those," echoing Tim Allen's fixit man character in Home Improvement (who often wore a toolbelt).
 * Slinky-Dog says "I'm not a smart dog, but I know what roadkill is.", parodying the line "I'm not a smart man, but I know what love is." from Forrest Gump, another movie that starred Tom Hanks.

Toy Story 3

 * Rex's roars in the opening are standard Jurassic Park T-Rex roars.
 * A brainwashed Buzz's "spend a night in the box" monologue, "the box" being a covered sandbox.
 * A plush Totoro toy appears as one of Bonnie's toys in Toy Story 3. (It should be noted that Pixar has done the English dub of every Miyazaki movie since Spirited Away, and Lasseter is close friends with Miyazaki himself.)
 * Miyazaki is referenced even in the credits with a "special thanks".
 * Right before the preschool kids burst into the room, some smaller toys are hiding and quivering under a cabinet, mirroring Tin Toy
 * Many people have made note of the similarity between Big Baby and the terrifying, doll-like baby in "Tin Toy". They even make the exact same sounds!
 * The evil cymbal monkey had to have been at least partially inspired by Merlin's Shop of Mystical Wonders.
 * Look quick at the books Andy packs away and you'll spot the title of another sad movie about a nonhuman who loves his owner unconditionally and went to great lengths to find her again.