The funniest part is when Sulley saw the garbage being crushed and compacted. Sulley made those weird faces and fainted repeatedly. 
Of course, the most touching scene is the final scene. It’s one of the best movie endings ever.
The credit is also funny. I like how Pixar put Rex the dinosaur there. 
I completely agree with you on the second reason Killer123. Welcome to Pixar Planet as well.
hehe, I think my fav moments have been repeated by a lot of people already! But here goes a few off the top of my head:
-Sulley’s reaction to Boo being “crushed”. I like this from an animation point of view especially, because of all Sulley’s varying looks of horror! Too funny! I think it’s also mentioned in the commentary that they “stole” that little sequence from a short toon. I have been trying to look it up ever since with no luck!
-The entire scene with Randall and Fungus introducing Mike to the Scream Extractor. Especially the beginning, when Randall is snapping “Yes, I got the kid!” and Fungus’s happy “Huzzah!” Oh, and also Randall’s folded arms reaction to Mike’s: “…it’s creee-tin…” line XD
-Mike and Sulley’s reaction to seeing Boo and trying to hide it from Celia at the Sushi place. I love Mike’s gaping expression, and Sulley’s lame excuses to Celia.
-I like the scene between Randall and Waternoose when they finally have Boo at the Scream Extractor; only because we rarely see those two monsters communicating anyway, which is interesting since they are both in on the scheme. I guess Waternoose was trying to keep his distance from it all, and not have to do the dirty work so much. Anyway I like Randall’s snarly reaction when Waternoose says “Sullivan was twice the scarer…” bit. Go Randall and your grrs!
-randomly, I like that pink monster that works as a Scare assistant. You know the one, he’s like a little slug thing. Cuteness.
I have plenty more favourites of course, but won’t bore you! 
My favorite part was when Mike says “Put that thing back where it came from or so help me” and then everyones looking at them. They then explain its for a play and they start singing.
I also like when they’re running from Randal and they jump in the door on the floor. Then the gravity shift makes Mike hit the floor and he says “that was weird” and then Sully lands on him.
I really like the part when Boo laughs and all the lights explode and Sulley’s like “What was That ?” 
And I love all the parts with Randall in it…
I don’t know if i’m the only one thinking this but in every film the “villain” is so intelligent, well i don’t know i find all the villains AWESOME !
Like Hopper in ABL, Scar in The Lion King, the white cat in Cats And Dogs xD I don’t know they’re are just so cool…
I like the part in the apartment, when Boo sneezed at Mike and he sprayed his eye.
I find the part in the garbage-masher-thingie hysterical still to this day. xD
I got another one.
The scene that Boo was sleeping on Sulley’s bed.
It’s actually not the scene that I like, it’s the soundtrack. In the OST CD, it’s the 11th song called ‘Boo’s Tired.’ The similar melody is also at the ‘Kitty has to go’ scene. The song almost made me cry, thanks to Randy Newman.
FONY, that’s one of my favorite scenes too! I absolutely love watching Sully’s facial expressions change as the scene progresses.
Needleman: So then I said, “if you talk to me like that again, we’re through!”
Smitty: Aah! What’d she say?
Needleman: You know my mom…she sent me to my room.
That’s probably my favorite part of the whole movie.
Mine, too! That line is so funny, and yet so realistic…you’d be surprised how many times I’ve overhead almost identical conversations between various guys right here in the Human World!
pitbulllady
My favorite has to be when they’re at Harry Hausens’s and Boo yells, “BOO!” an all the monsters freak out
I have a few favorite parts in this film.
-The fight between Sulley and Randall towards the end. Every thing about it was just brilliantly awesome, good words between the characters. Loved, loved the fight.
-The scene between Mikey/Sulley in the snow and Abominale Showman. It was just emotional and funny at the same time. Really showed some thing here.
-The chase at the end between Sulley/Mikey V.S Randall, trying to get Boo back to her door. Loved every thing about these scenes.
-Boo gathering her fear, attacks Randall to save Sulley.
I have way more, these are my top.
I haven’t seen this movie in a while, but I remember my favorite part was when Boo was in the bathroom stall singing. XD It always cracked me up. 
When Sully passes out three times in a row at the thought of Boo getting crushed,
When Mike sprays himself in the eye with the disinfectant,
are my two favourite bits , love the whole movie though its great
Randall: “What are you two doing?!”
Monster: “They’re rehearsing a play.”
Mike: singing “She’s out of our haaaiiirrr…”
Randall: “Can it, Wazowski!”
Randall: “What happens when the whistle blows in five minutes?”
Mike: “Uh, I get a time out?”
Randall: “Everyone goes to lunch! Which means, the scare floor will be…”
Mike:“…Painted?”
I’m going to settle on 3 moments:
For heart: When Sulley and Boo hug goodbye - that moment of her little hand petting Sulley’s face gets me every time.
For thrills: The entrance to the climactic chase with Mike and Sulley riding the door, the moment when they and we get our first good look at the door vault - that awesome “Oh, my gosh…” moment before the “roller coaster” takes off.
For laughs: When Waternoose is caught red-handed in the simulator room, and Mike says, “I don’t know about you, but I spotted several big mistakes. Let’s watch my favorite part again, shall we?”
Strangely enough, one of my favourite bits of the film that I haven’t yet mentioned is actually the title sequence. I love the fact that it’s in 2D and the style of it is just so…Monsters, Inc.-ish. Always makes me happy to watch it.
My favorite part is when they are in mike’s apartment.
All that scene and when Sully goes to bed boo.
In all the scenes from General Sully and Boo.
when everybody got scared when Boo yelled boo in Harryhausens