Some of the Quadro cards support stereo. The cards that have an output called "stereo" under "Display Connectors" listed at Nvidia's Quadro overview page have a 3-pin DIN outlet that fits with NuVision or CrystalEyes stereo glasses.
The cheapest of these used to be the FX1400, but now appears to be the FX3450 (around 750 €). These cards are by far fast enough for protein crystallography or modelling.
For stereo, the xorg.conf might need the following lines
Section "Extensions" Option "Composite" "Disable" EndSection
if the X log file (e.g. at /var/log/Xorg.0.log) says that stereo is not supported by composite.
Another option that will be required in xorg.conf by programs running stereo is
Section "Device" Driver "nvidia" Option "Stereo" "3"
You also need to set the environment variable STEREO for the stereo to work properly in ono: setenv STEREO on (tcsh) STEREO = on; export STEREO (bash) 
Mac OS X
The following command needs to be run for Macs to be able to support stereo in X11 programs, such as Coot  :
defaults write com.apple.x11 enable_stereo -bool true