The above two are made with flash and 3d-flat-objects....the objects are rendered with a 3d-editor or they just flat images with depth in it. (using Photoshop). the other is made by flash, also just using ONE 3d-element rendered by Flash (the candle)...the rest is just an animated background with depth in it. You can also do this by just drawing a box existing out of 6 squares in photoshop, you then alreadsy have got a 3d element.... GIMP allows you to even turn a photo into a turning ball. there are many sites who use 3d.. some of them just don't get noticed. I know MANY designsites who act like a 3d-environment...they are really nice and it's fun to walk through a world, searching for something to use....
Banners are the most used 3d-elements, because they are simple to make and make a good impression to users of a site