[spoil]It’s not in the train sequence that I can tell. The score from when Buzz “flies around the room his his eyes shut” is used there. Having listened to the soundtrack several times, I don’t think the whole theme is used anywhere. The first three notes or so are used a fair amount, just as they were in Toy Story 2, but I don’t think it’s used anywhere in it’s entirety. Though a ton of score is missing on the soundtrack, so it could be hiding somewhere else. But I’m not really sure.[/spoil]
“One-Eyed Bart” (first) and “Evil Dr. Porkchop” (second) is one I found that played as a parallel. Also, Death by Monkeys and “the wife and tater-tots” (even though that wasn’t said directly).
Another one is that I find interesting is how [spoil]Molly is persisting to get Andy’s room and stuff, and it shows them sharing a room in the first movie.[/spoil]
EDIT- Please use spoiler tags when referring to what happens in Toy Story 3, even with minor things, thanks!
-lizardgirl
I’m watching Toy Story 2 tonight and I caught something that is referenced (and almost parodied) in Toy Story 3.
In 2, when Al steals Woody, Buzz leaps to his rescue by sliding down the the drainage pipe on the side of the house, and then hides behind the mailbox so he won’t be seen.
In 3, [spoil]when the toys end on the curb, Woody slides down the same drain pipe to save them. He’s not as successful as Buzz, though, since his bumps the gutter and falls into the bush below. He does, however, hide behind the mailbox so he won’t be seen.[/spoil]
Sorry if that’s really obvious, but I thought it was interesting.
Then when all the gang [spoil]returns to Andy’s, they use slink to go up that same ledge of the roof they left on to go rescue Woody. Also, in the “When Somebody Loved Me” sequence, there’s a shot of Jessie in Emily’s hand, with the light looking all “magical” and bright from the sun, and it looks a lot like the shot right after Andy hands Jessie to Bonnie, where Jessie is in Bonnie’s hands.[/spoil]
Hmm. I remember something I didn’t catch the first time I saw Toy Story 3:
The first line in the film is from Potato Head/One-Eyed Bart, who yells, [spoil]“Muwah ha ha! Money Money Money!”[/spoil] The same thing Andy had him say in the opening of the first Toy Story.
in the first Toy Story, when sid gets woody and buzz, he says “lets go home and play.”
in Toy Story 2, after Woody and Jesse get off the plane, woody says “lets go home.”
–
something pixar should of done in beginning of toy story 3 is when ever Mr.p says “im a married man”, he should of said “im a married spud.” 
I’m really happy with all of the mirrored scenes in Toy Story 3! As I was watching the film I kept seeing the connections and it made me really happy 
Toy Story 2, ‘let’s leave Buzz to play with his toy’
‘toy, toy … toy!’
[spoil]Toy Story 3 ‘what’s the point’
‘point, point … point!’[/spoil] - when in the [spoil]trashbag[/spoil]
or something along those lines??? ^
Yep, I noticed that one too!
Another one:
[spoil]Woody: Think, think! Ooh!
whistles for Buster
- occurs in both Toy Story 2 and 3.[/spoil]
Might have been said already: but [spoil]In TS3. you see Andy making Buzz and Woody slap hands while playing with them, then Bonnie makes a similar gesture with the two of them at the end.[/spoil]
Andy also did a similar thing in the first movie’s opening - “Yeah, cowboy!”
something i think is the same but not sure is:
in toy story 1, [spoil]woody prevents Sid’s door from closing with his hand[/spoil]
in toy story 3, [spoil]when woody is at sunnyside and escapes (1st time), he prevents the door from closing once again [/spoil]
[spoil]Woody and Buzz’s symbolic handshake from the first movie is almost re-enacted when Woody leaves Sunnyside (except Woody rejects it), and at the end.[/spoil]
Toy Story 1: Woody panics and becomes inanimate when he sees the truck approaching him at the gas station.
Toy Story 3: [spoil]Woody panics and becomes inanimate when he sees the cleaning cart approaching him.[/spoil]
This might be slightly off-topic, but don’t you think the scene when Mr Potato Head is thrown into the sand box by Big Baby (not a spoiler since it was in the trailer), shot in the same manner as the last scene in Saw? I might be wrong, but I always thought it looked identical to that scene; especially with Potato/Adam’s hand sticking out.
At the end of Toy Story 3 [spoil]Bonnie has Buzz and Woody do their “Secret handshake”[/spoil]
Pretty sure this hasn’t been mentioned yet.
Toy Story opens with pulling out to show Andy’s Cloud wallpaper.
Toy Story 3 [spoil]closes with zooming into the sky, where the clouds resemble Andy’s old wallpaper.[/spoil]
[spoil]I thought it was a really nice touch, sort of a sting of nostalgia, and it brings it “full circle” in a way.[/spoil]
EDIT: I noticed that in the Tram Chase scene in TS2, when Woody grabs onto the tag, it is about the same width as the strap on the Moving Truck, and when it speeds up, his legs flail very similarly to how they did when he slipped down the strap before Scud bit him.
I just realized, and this is probably coincidental, but in the first Toy Story Sid’s Mutant Toys Fixed Buzz by putting his arm back on. In TS3,[spoil] Lotso’s Gang “Breaks” Buzz by putting him back into Demo mode.[/spoil]
EDIT: For some reason, it put my spoiler bold instead of Spoiler.
BTW, with my little theory about the mutant toys, I’ve made a new lead; someone on Pixar Wiki mentioned that [spoil]the frog on the garbage truck could represent The Frog.[/spoil] Which means so far there’s;
Big Baby > Babyface
Twitch > Rockmobile
Jack-in-the-box > Hand-hand-in-the-box
and now [spoil]garbage truck frog[/spoil] > The Frog
The whole scene of woody grabbing the tag from standing on bullseye is also similar to [spoil]him boarding the train to save the infants[/spoil]