Hey I would like to know if anyone knows what the most effective and efficient way in making a 3D video using such programs as Cinema 4D or Maya.
I did some internet searching but nothing interesting.

Trying to create a simple 3d animation such as the Nvidia Stereoscopic Setup Video. (rotating logo)

THX in advance!

The basic idea is to create a node (dummy object or whatever) and add two cameras as children of that node. Arrange the cameras so they are slightly apart on the X axis, about 65mm if possible. Of course you might be going for hyper-stereo, or you may not have a predefined scale, so you can do this by eye if necessary. Then you simply animate the parent node for any camera movement. You may also want to create a focus node, then have each camera locked to look at that node. This will allow you to animate the focus (convergence) on the fly. Then you would have to render the scene twice, once for each camera. I think this setup should work alright, but I admittedly never attempted to do this.

UMM wow
it shouldnt be that hard haha. But that could also have the best result.
Okay so then after rendering the 2 video's (one from each eye)
How would I be able to make the proper effect of rendering both together.
Thanks for you help cybertron!

If you want to create stereo 3D animations at a low cost you can also use Blender, which is free. Here is a video tutorial about stereo rendering using Blender :
http://www.vimeo.com/15671492

OR, if you're too lazy to set up your own camera rigs and have some spare cash you can use SVI plug-ins.

After you have the two renders then use Stereo Movie Maker to compile them into a side-by-side, anaglyph or whatever 3D format you need.