I think I figured out how to render equirectangular (360x180 degrees) stereoscopic (3D) images sequences with Blender!!! Well...technically other people figured it out and I just put the pieces together.
Here is the full sized rendered image to try for yourself in Whirligig.
Blender 2.72b http://www.blender.org/
noeol's Stereoscopic Rendering Blender script 1.6.9 http://www.noeol.de/s3d/
VirtualDub 1.10.4 http://www.virtualdub.org/
Whirligig 1.47 http://www.centzon.co.uk/whirligig/
There's basically 2 steps involved. First you setup an equirectangular lens on Blender's camera. Then you convert that camera using noeol's script into a stereoscopic rig.
To setup an equirectangular camera lens you must first set your render engine to Cycles Render. Then select your camera and in the Lens section of the camera Settings choose Panoramic with an Equirectangular lens type. You won't see the Lens Type setting if you don't change the render engine to Cycles. That's it, try rendering a frame. Use something like FPSViewer http://www.fsoft.it/panorama/FSPViewer.htm
to view the 2D panoramic image.
After setting up your 360 camera, you need to convert the same camera into a 3D stereoscopic rig. noeol's script is freakin' awesome for this. He has a great youtube tutorial on his website. WATCH THE VIDEO. Seriously. The whole thing. You're gong to be using the Side by Side stereoscopic preset and there are special instructions just for that one.
After you set it according to the video and you hit render, Blender's image viewer won't be able display the whole image but it will output the full image file to a directory you selected previously (during the video tutorial that you totally watched). If you render out an animation, you will get a sequence of images in the chosen directory. You can use VirtualDub to import that image sequence and export an AVI. Just drag the first image of the sequence into VirtualDub's main window, change the framerate to whatever you want in the video section, and save to AVI. Your video is now ready for viewing in Whiligig or LiveViewRift.
I just pieced all this together last night and its very much a work in progress. But I do think I'm on the right track here. If anyone has anything to contribute please do! There's a lot of discussion on this topic in another thread here, but its more focused on Maya/Max/MentalRay. I hope this helps some one else.
It appears that some one has solved the problems and streamlined the process. Hopefully, it will be officially supported in Blender soon. In the meantime, check out the website below for an explanation and patch.