I made some progress with my ACER GN245HQ on the subject :
DVI 3D mode can now be activated with the correct modline in xorg.conf and then activate the IR emitter with a3dcontrol.
After some experiment with nvidia tools to create personalized resolution and synchronization I found that to activate3D stereo modeIi have to change the number of vertical lines. It must be greater than 1147 1150 is the max supported.
I used then powerstrip on windows to extract the modlines while 3D stereo active or not.
1080p 120Hz without stereo modeline:
ModeLine "1920x1080_120.std" 285.545 1920 1968 2000 2080 1080 1083 1088 1144 +hsync +vsync # standard
1080p 120Hz stereo modeline:
ModeLine "1920x1080_120.3ds" 286.754 1920 1968 2000 2080 1080 1083 1088 1149 +hsync +vsync # stereo
When this mode is active a3dcontrol permit to activate the integrated emitter via I2C.
So it should now work with nouveau (don't know if I2C easily available with nouveau).
Here my xorg.conf : http://a3dcontrol.googlecode.com/git/X11/xorg.conf
Next step is to try to activate IR synchronously with right or left eye display, to prevent eye inversion at startup.
After that I'll try with nouveau and with an intel integrated GPU.
I would also like to find someone with asus 3D Vision 2 screen to extract modlines while 3D stereo active and inactive and to known if the same technique is used to discriminate 3D content.