In any form of design, I believe the devil is in the details. This is demonstrated beautifully by sites that use a three dimensional esthetic. A really good example is squaredeye.com (let’s be honest, mainly because I think the whale is cute). I think most people can appreciate the time and skill that goes into making any three dimensional web design.
Despite that, not all sites that use three dimensional techniques are for the better. You can go too far with it. Take for instance, this site. I find it hard to navigate because I’m so caught up in the 3D boxes. It actually kind of hurts my eyes to look at!
While I don’t necessarily think a website has to utilize 3D techniques to have a great design, if you are going to choose that route, do so with discretion. A great subtle example is riotindustries.com. The left hand navigation really shows the skill of the designer, without being too in your face. 3D or not, it’s all about those subtle details that make or break your design.