Loads of the Pixar movies have me welling up in places, but as Speak Softly said further up, Toy Story 3 had me (and still has me) completely bawling. The bits when the mother is packing up Andy's room to send him to college, and we've watched this kid grow up over the years, well, I have that to come so that really gets to me.
But the bit at the end, when Andy is giving his toys to the little girl, and he gets to Woody, and he's describing what a good friend he has been to him all his life, but he knows he's grown up now and doesn't need him anymore, but he still clearly loves him, WAAAAAH!!!!! Absolutely brilliantly done.
And when they watch him drive off, and Woody's "So long, buddy....." I think Toy Story 3 is the best of the 3 movies - and that's saying something because all 3 are absolutely superb.