Kavuri Sateesh of Intel published the first of the Linux DRM patches concerning 3D support for HDMI monitors. Right now what the patch is doing is enabling support for reading the 3D capabilities of a connector monitor over HDMI, but Kavuri says similar functionality could be implemented for DisplayPort and the Embedded DisplayPort interfaces too.
From his mailing list message, "the idea is to read the 3D capabilities via EDID and provide this to a user space application that would want to switch the mode of the connected monitor to a specific 3D format. The implementation follows the HDMI 1.4a specification."
Expect more work in this area soon.