CGI, also known as 3D animation, gets a bad rap. Some people simply feel that more traditional methods are superior, while others don't mind innovation, but don't think that CGI has been executed particularly well so far. While there are definitely some bad examples - the 2016 version of Berserk that aired on TV comes to mind - CGI can be used to beautiful effect.
The best anime with 3D animation doesn't just choose the technique for no reason. 3D animation is used intentionally, either to smooth out action sequences, to underscore science fiction or supernatural characters and themes, and more. Some of the best 3D anime include Land of the Lustrous, The Count of Monte Crisco and Ajin. Without CGI, these anime would have a markedly different look and feel, and might not be quite so remarkable.
Let's give a shout out to the anime that best used modern technology to its advantage.
Not every entry into the Fate series makes good use of CGI, but ufotable, the company responsible for Fate/stay night: Unlimited Bladeworks and Fate/Zero, uses it to beautiful effect. ufotable combines 3D animation with photography, 2D drawings, and other special effects to make the incredible Holy Grail Wars come to life. The bloody, intense nature of the story itself won't appeal to all viewers, but it's hard to argue with the visual quality.
Ajin is a Netflix exclusive anime about a new species of human that possesses a panoply of special powers, including immortality. Because they're labeled as a threat, anyone found to be an Ajin is immediately arrested. When Kei Nagai gets into an accident that should have been fatal, he realizes that he might be a member of this mysterious species. This is a compelling story, but how's the animation? Actually pretty good. The reason for this is the frame rate. Some anime swap out 3D animation for 2D animation regularly, and the resulting shift in frame rate speed can be jarring. Because Ajin relies solely on 3D animation, it's able to be consistent.
You can't talk about 3D animation and not mention Land of the Lustrous - it's one of the stand-out anime of 2017, and it's one of the most effective uses of CGI in the medium's history. While the characters do not look human, that is an intentional choice rather than an off-putting mistake. They are humanoid gems whose bodies don't operate the way that human bodies do, and the CGI does a great job of getting that message across. Still, shots appear to be drawn in 2D, while the animation itself uses everything that 3D has to offer to create a rich and beautiful world. Not only that, but the story it tells is wholly unique - the whole gem thing might sound like Steven Universe, but its tone and themes could not be more different.
Gankutsuou: The Count of Monte Cristo mixes Alexander Dumas' classic novel, The Count of Monte Cristo with sci-fi elements, so if you're a literature buff, it's a must-watch. But even if your favorite class wasn't AP English, you can still appreciate this anime for its incredible blend of 2D and 3D animation. The characters are traditionally drawn, but everything from the backdrop to the characters' clothes are rendered in 3D, creating a unique visual experience that can't be found anywhere else. The style perfectly mirrors the content - a marriage between tradition and innovation.