From WALL-E comemntary:
something like
Andrew Stanton: We have have now reached a point in the commentary where I have nothing to say for the next minute.
From Nemo commentary:
while showing the Disney logo at the end
Bob Peterson (I believe): And the secret of life is… (movie ends)
From the TS2 commentary:
Ash Brannon (talking about Zurg): I’m kinda glad that our villian wears a skirt. (all laugh)
Yeah, I love that “3D money shot” line. Bob is great. Not exactly a quote, but I loved the discussion about Bob coming up with Dug’s “I can smell you” line, and Pete thinking “Huh??” and not thinking it would work. Oh, and following on Flik-E’s post - I am so glad Disney named the hero of “Meet the Robinsons” Lewis, (that’s the discarded name and the other movie involved) because Russell does not look like a Lewis, he looks like a Russell!
So Russell was going to be called Lewis at one point. That’s pretty cool. 
One thing I knew about Meet the Robinsons is that John Lasseter was the one who came up with the T-Rex saying his arms are too small (taken from Rex of course) so that’s the other connection Pixar has with that film.
My other favorite line in that part of the commentary was when they point out how they randomly have a lever in Muntz’s blimp that tilts everything around.
Yes! That, too! The whole Up commentary is great because you can tell that Pete and Bob are having so much fun.
In the Art of Up book is an early line-up of rough sketches that shows the basic shapes of the main characters, and Russell is labeled as “Lewis.” (Also, Ellie is labeled as “Eleanor,” and is also referred to as “Eleanor” in another sketch in the book.)
I love Andrew Stanton’s countdown to fill in that gap in the wall-e commentary.
but I love Bob Peterson’s chips in Finding Nemo too. 
to be honest I haven’t seen all the movies with commentaries… they’re very hard to find but I do love in toy story 2 when, I think is andrew stanton says that the villan wears a skirt… and also love the ending when they say we have to go finish monsters inc.
When that came up, I immediately had to think about Yzma’s famous “Wrong lever!”/“Why do we even have that lever?!” lines from The Emperor’s New Groove. 
Yet another reason why Nemo has one of the best commentaries I’ve heard
Just got Toy Story 2 Extended Edition, listened to the commentary and didn’t really hear anything that caught my attention.
I disagree. 
John Lasseter: I love Hamm’s introduction because of the whole notion that lawn gnomes are alive as well; it just cracks me up.
Lee Unkridge: I think we need to do a whole movie about lawn gnomes.
Somebody: SHHHHH!
LU: Oh.
Somebody: Sorry.
JL: LEE?!
LU: I’m fired, aren’t I?
Andrew Stanton: 
(Gee, I wonder if Gnomeo and Juliet was in early development at the time…) 
AS: I just love death by monkeys.
Ash Brannon: When in doubt use monkeys and you’ll be fine.
LU: That’s the credo I live my life by.
JL: That’s right. Lee loves monkeys.
(This might explain why the main characters are being chased by a stampede of monkeys in one Toy Story 3 sequence.)
JL: The dashboard is amazing on that car!
AS: They do it with computers.
I love Stanton’s cynical sense of humor about computers.
At the very end of Monsters, Inc. too, when Lasseter and Stanton start snoring and then suddenly wake up:
AS: Look it there’s the castle already… quick before the Luxo lamp goes out say something profound… computers are really cool!!!
I just love all of the Toy Story 2 commentary, so take any quote from that. I seem to find myself constantly referencing it in my posts.
Oh gosh… it could take me a while to remember all the greats! I mean, I love every commentary! I recently got to see the Cars 2 one for the first time and I loved it, too; just wish I remembered at least one great line… 
If I had to pick a fave commentary, I might say the one for TS2. That one must’ve been so much fun to record! I know that whenever I get involved in animation, I’ll jump at any chance to get on the commentary! If I haven’t already made that clear, I love commentaries!
I dont have the exact quote but I remember on the Nemo commentary when Andrew Stanton was getting teased for being on an after-school special called Dear Diary. Actually the Nemo commentary is still my favorite for being full of funny moments like that. Another was when they said Charles Nelson Reily was the 2nd most deadly creature in the world. 
This isn’t for a feature, but if any of you have Pixar Shorts Volume 2, check out the George and A.J. short with the commentary. I won’t spoil it, but it’s with Josh Cooley and someone else whose voice you’ll probably recognize. It’s quite funny!
I also like the Mr. Incredible and Pals one, which I know isn’t a main short, but it’s still funny to hear Frozone’s ranting.
So reading this made me realize how much I’m missing out. My life needs more Pixar commentary!
I can’t believe I forgot to mention this one sooner. Straight from the Brave commentary, I don’t actually remember who said this, maybe Mark Andrews? There were a lot of folks on it. But talking about the sounds of the will’o the wisps, which have some sounds of whispering children integrated in it:
“…'Cause nothing’s creepier than children whispering… unless it’s clowns whispering.”
^ That was my favorite line in the Brave Commentary.
I still need to check out the Brave commentary.
The A Bug’s Life commentary, where they start talking about how they’ll probably end up using John Ratzenberger in every movie, and how the Pizza Planet delivery guy lives in the trailer near the bug city. In hindsight, both comments are hilarious.
And the part of the end credits, where they’re discussing how no one has any idea how they make these movies, so the outtakes will confuse everyone even more.