I am new to all this (still figuring out how Linux MCE works) but I believe 3d is already suported...
Maybe if you are using NVidia 3D-Vision or something similiar it wont work because something have to control the active shutter glasses, but if you are using 3d projectors as you suggested I believe you only have to configure the projectors.
I've been playing around with a LG D2342P 3D-Monitor for a few weeks, I've downloaded and played 3D videos in kubuntu without the need of any additional software, the movies I tested are normal video files with twice the width and both images side by side, all you have to do is force 16:9 and activate full screen in whatever player you like, I also tested interlaced image videos, the 3D magic is made by the monitor itself, you do need to select what type of 3d you are trying to watch in the monitor options but nothing different is done by the computer, this projectors or a 3D tv will work the same way. I still haven't connected the MCE machine to this monitor to test this hypothesis, but as my xbox outputs 3d video in the same format (side by side in 32:9) I am assuming this is the standard for 3d video and I don't see why it would not work in a normal installation of Linux MCE.