I don't think there is much you would do on the AE end in that case short of interleaving the sequence at double the target frame rate. The rest is pretty much up to the way it's being shown via projectors or on screen and how the software/ driver that triggers the display. Only when it requires specific types of interlacing/ alternating dithering would you need to take additional steps...
Ah... I didn't think about the frame rate! that's a good point, So if I'm working on a PAL video which is 24 fps I would just have to create a 48 fps video with alternating frames of the left and right views? Now comes the expensive part of buying a Polarized monitor. Should be worth it though as its meant to give much better results than Anaglyph animations.
If you are using "polarized" monitors, then there are also new monitors around (46" from JVC and Hitachi), which are capable of using side-by side or interlaced content, without the need of active shuttering - and therefore frame rate - issues.
Side-by-side here has the disadvantage of using only half of the horizontal resolution (you have full HD in standard mode, but only 960x1080 per eye in SBS mode) content creation is very easy using the builtin AE features (3d glasses effect). You just place left and right camera's eye view side by side on the Full HD resolution canvas using the filter, the monitor takes care of putting the pixels to the appropriate polarization filters (circular) if set to SBS mode.
I have one to play around now and it is fun... and you can use cheap, passive glasses technology and cheap playback deviced such as CF card players also...