How are 3D websites made?

My background is with traditional SEO and W3C methods of design and development, using CSS, Php, XHTML, etc.
I have experience with Flash as well, but mainly used it to spice up my traditional pages.

I have been seeing many sites created entirely in flash, which is fine though I know some people frown on them.
My main interest is in some of the sites that I have seen on template monster that incorporate 3D models, and effects that are very much like the "Northern Lights". Also, I have seen sparkles used quite often, whether over buttons or orbs that float around.

Can someone explain how this is accomplished? I cannot seem to find much throughout my googling that leads to a direct tutorial explaining how it is done.
My thought it is that it incorporates Flash, Swift 3D, Photoshop, After Effects, and models from other programs such as Studio Max, Maya, Lightwave, etc, if they were not created in Swift 3D.

While I have dabbled in many of these applications, I still do not understand how they are directly applied to each other, or what the best practices are. It would be nice to find a tutorial that clearly defines what to look out for, and not to do so that the site is optimized, etc.

Thanks

Can you put up some links to examples of what you are talking about?

http://www.ozzu.com/designs/flash_templates/template_number/23535/

Thanks

Yes its little bits of After Effects brought into Flash as either an image sequence or a short video file. I doubt its even using any thing from a 3D program.

Good tutorials for similar effects are available from http://psd.tutsplus.com/ and http://ae.tutsplus.com/

"3d" is not really the best term in my opinion, the browser is not rendering anything or creating light effects, its still just pictures. 3d in a web site sence (in my opinion) is using z-index to get x (being width) y (being height) and z (being stacking things ontop of other things)

but getting a 3d look generaly means rendering 3d objects with a 3d program (I use Rhino as its simple, easy and was cheap.) and saving it as an image (.jpg etc) then putting them into photoshop or a pic editor to create exactly what your looking for. then positioning all your pics on the page creating the look, Or in flash. I've used swift 3d for flash stuff, cool little program, it works by making slides of the object to be pasted into flash. (or atleast ver 2.0 did) its bascily a simple object animator with preset motions.