Wonderful Days (Sky Blue in many parts of the world) has some great CGI backgrounds, although the characters are 2D cell animation.  It's an awesome piece of work.  The Appleseed movie of a few years back is visually excellent, and quite good storywise.

Fifty Percent Grey and The Cathedral (both on The Animation Show: Volume 1) are both excellent 3D shorts.  Volume 2 has Fallen Art (by the same director as The Cathedral) and Rock Fish, both of which are highly regarded.  Check out some of the stuff from Blur Studios, they do some great work.  Some of their stuff (and other great 3D stuff) is available, among other places, from Stash Magazine.  Also check out the following:

Elephants Dream
Cee-Gee (my fave being The Hunt).

If you want a bit of retro, some of the scenes in The Lawnmower Man look pretty dated.  I think the TV series Reboot is out on DVD too.

...and since you referenced the stop-motion stuff, if you want something with both, the TV series Lavender Castle has great stop-motion characters with (pretty poor) CGI backdrops/vehicles.

Then of course there's the mainstream studios, but I shall leave them be.

Quoting W0m6at:

Has anyone watched Appleseed: Ex Machina?  The first movie was excellent, and I'm getting impatient waiting for my copy (it was delayed because of something else in my shipment... but it's on the way now).  It'll be great to see what can be done a few years on.

I am not an aficionado of anime, but with the reviews I saw I thought what the heck! All I can say is this is really impressive - the story had emotion to it and the blu-ray was top quality!