Okami has been mentioned, and yes, it does really well in that game.
I liked the use of cell shading in XIII, I think it did a pretty good job to make the game look like the French Graphic Novels. Now if only they hired someone other than David "I have no soul or emotions" Duchovny to voice XIII, things would have been a bit better. But keep Adam West, his campiness helps all!
Another great game was the Sly Cooper series. The Cell shaded aspect worked to make the game look like a Saturday Morning Cartoon. Everything had an interesting "Mid-90's" look to it.
No More Heroes also works well. The over-the-top violence can be made into humourous activities when the whole place looks like a cartoon. The game has an odd, 1980's notebook sketch feel to it all, as well as making the world look like a cartoon through the anime fan hero's eyes. Granted, one cannot mention NMHs without also adding Killer7, which made the game look like a bizarre bit of abstract art rather than a traditional game.
Cell-shading, like everything else, is a tool, and should really be used if it will actually help the mood/plot/characters. Several games out there seem to just put on the Cell-Shading filter and thing that it'll be fine, but honestly, it doesn't seem to work that way.
Granted, I'm not mentioning how good/bad the games are, I'm just saying the cell-shading worked well for the mood the developers were trying to put across. Honestly, it was a bit jarring in Samurai Champoo: Sidetracked to see everyone in hyper realistic 3D models rather than the stylized, unrealistic anime models.