-John Lasseter
I know there might have been some sequel discussion in one of the general Pixar threads, but I'm not sure where it would be...
With Toy Story 3 having been out for a bit, Cars 2 coming out as I write this, and Monsters Inc. 2 (Monsters University) coming in 2012, I figured this was a good time to talk about PIxar sequels.
Disney commissioned Toy Story 2 as a 60 minute direct to video work, but Pixar started from scratch to make the feature film we know and love today...
Also, despite a Gentleman's Agreement that Disney wouldn't make any Pixar sequels without their involvement, Disney started pre-production on Toy Story 3 after the two were unable to agree on a new deal. Of course, all that is moot now with the merger, and Lasseter in charge of ALL Disney and Pixar animation.
Toy Story - they did a great job with Toy Story 2, I haven't seen 3 yet personally.*
A Bug's Life - I don't know that a sequel is really needed.
Monsters Inc. - A Prequel is coming (Monsters University), I think a prequel OR sequel would be welcome. I think the interaction between Boo and the monsters was great, although a prequel would miss out on that. A sequel where Boo might be old enough to not believe in the monsters could be interesting, although it's not a case where the monsters would dissappear if enough kids don't believe. Plus, that might borrow some from The Santa Clause 2 or 3.
Finding Nemo - I don't know that a sequel could do much without retreading the same ground... Of course, I am probably one of the few Pixar fans that didn't really care for the film.
The Incredibles - I could easily see a good sequel to this, Superhero movies have sequels, and the family could have another great adventure or two.
Cars - Along with Finding Nemo, this is one of my least favorite Pixar films, and I don't really know where they are going to go with the sequel.*
Ratatouille - While I love the movie, I think the first one wrapped the story up pretty well.
WALL-E - Again, I don't know that the story would have a lot of room for a prequel OR sequel. A prequel - Wall-E cleans up garbage, alone or with other Wall-E units.

Up - The same thing goes for this, sure the old man (and the boy scout, dog, etc.) could have further adventures, but I don't know if they would really fit with the theme of Up.
*Please try to keep major spoilers for Toy Story 3, and particularly Cars 2 (since it's JUST being released) out of the thread...