I have someone taken intial steps to solve this issue. I have remixed an additional encoding of the left channel as its own video channel.
# SIDE BY SIDE
ffmpeg -y -i "movie.mp4" -i "movie.mp4" -map 0:0 -aspect 16:9 -c:v:1 libx264 -q 0 -vf stereo3d=sbs2l:ml -s 1920x1080 -map 1 -c:v:1 copy -c:a aac -strict -2 -ac 6 -ar 48k -ab 640k "..\3D\movie.mp4" -sn
# OVERUNDER
ffmpeg -y -i "movie.mp4" -i "movie.mp4" -map 0:0 -aspect 16:9 -c:v:1 libx264 -q 0 -vf stereo3d=ab2l:ml -s 1920x1080 -map 1 -c:v:1 copy -c:a aac -strict -2 -ac 6 -ar 48k -ab 640k "..\3D\movie.mp4" -sn
In the short term it would be pretty simple IMHO if Plex just provided support for selection of multiple video feeds. Currently most clients just play the first stream.
The video provides both representations of the stream. Stream #0:0 is the cropped/reencoded left channel and stream 0:2 the stereoscopic stream). If Plex could simply detect multiple video streams and provide a library entry for those additional streams, this would give us the capability to select from our current implementation which stream we want to see. I completely agree with the previous poster about allowing detection of tags within the video filename to show if its SBS or OU. Also, it would be nice if we could get an overlay on the image when browsing the library showing that the content was 3D when present... similar to the shortcut symbol placed on icons on windows machines, but maybe a black box with 3D written in it.
The real key is when streaming out to the client, plex should remux the video and only include the video stream that was selected. This could also be done on the client end where directplay is utilized by giving an option to select the video stream as we select the audio stream or subtitles.This could further be integrated by allowing you to create a library that has a checkbox upon creation saying it is either 3D for legacy implementations of the client (appliance/televisions) which only populates titles based upon whether they have a stream that has 3D content in it or not.
This concept extends beyond use within 3D as well. For example you could have multiple video streams for different views in a movie for example DVDs that have different viewing angles or non-theatrical cuts that are synced with the theatrical film.
Furthermore we're only preparing for features coming down the pike in FFMPEG. When the FFMPEG devs get stereoscopic detection complete then Plex could detect which stream is 3D. If the device could advertise that it supported 3D video to the plex server, then the server could simply not show content that contains 3D material in the response.
I noticed someone spoke to the concept of using -vsplit and -hsplit during the encode, I am thinking that this might be a dangerous concept because to my knowledge I don't believe you can just remux half of the stream back into the container as the dimensions and math for reproduction would be off. So this is most likely going to incur the cost of having to reencode the video on the fly which may work for 1 or 2 viewings at a time with a moderately powered setup, but it would be hard to support much more and could lead to a poor viewing experience by those not understanding the implications.
I've always maintained the thought that your library should be in whatever format is best for viewing on most devices so muxing can be used instead of encoding.