The film itself is one of Pixar's best. It certainly shows a new found maturity to their filmmaking, bringing my wife and (presumably) a good proportion of the rest of the audience to tears. I, on the other hand, am a Northern English bloke hardened by a childhood working 28 hours a day down the mines, bricks for breakfast, living in a puddle, etc - therefore no film has ever had that effect on me (either that or I'm just emotionally stunted). The fact that a frankly surreal story idea works so well is testament to Pixar's excellent storytelling craft.
As for the 3D effect - I'm not completely convinced it's anything other than a short lived gimmick. It certainly works - the form of objects is realised surprisingly well and the circular (as opposed to linear) polarisation seems to negate the headache I was fearing. However, I kept finding myself distracted by the 3D effect and wasn't able to completely absorb myself in the film. Perhaps this impression will fade if 3D cinema becomes more commonplace.
Another problem which the film mostly avoided is a perceived lag that happens when there is a camera cut. Pixar seemed to be vary careful to keep the amount of parallax on the focus of the image roughly constant between cuts, but the editing on one of the trailers beforehand (some 3D CGI space thing) was jarring. Far too many fast cuts causing a noticeable delay whilst my eyes locked onto the new parallax. Maybe younger viewers are able to keep up better, but I'm a 30 year old boy - surely my eye muscles are still good!
Reading this post back, I've noticed that I haven't (yet) mentioned the graphics in the film, despite being a graphics geek and indeed a graphics programmer. Suffice to say they're so good you barely notice them - the few times I did think about it I saw flawless lighting, shading, the works. Sometimes I envy film effects people in that they have a lot more processing time at hand as opposed to games aiming to have everything rendered within 16⅔ or 33⅓ milliseconds depending on whether we're aiming for 60 or 30 frames per second.
Another technical oddity I noticed is that at the end of the credits (I hung around in case there was any extra bits at the end), there was a message saying that all final rendering had been done on Intel processors. I'm mildly surprised that Pixar aren't using any GPU technology such as NVIDIA's CUDA or OpenCL to accelerate things - perhaps because the cost and time required to port over their existing rendering software is prohibitive, despite the gains, so simply throwing more processors at the problem is a cheap way to improve rendering performance.