Stereo

Hardware

Zalman Stereo

has its own article.

Nvidia 3D Vision 2

3D Vision Pro is not what you want, this is for professional CAD/CAM applications, and is expensive.
The quality of Nvidia 3D Vision 2 is better than that of Zalman, because Zalman stereo means halved vertical resolution.
The Nvidia 3D vision emitter must be connected to both USB and Quadro 3-pin DIN Stereo socket. This setup works on Windows and nowadays Linux. The cheapest (2014+) Nvidia Quadro with 3-pin DIN Stereo connector is the K4200 (http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at ~ €700.
For Linux, a Nvidia 3D vision emitter "workaround" requires the DIN 3-pin connector found on the high end Quadros and NuVision or CrystalEyes stereo glasses and emitter.
Consult this link, and search this link for the word USB.
Compatible Stereo monitors (120 or 144Hz with DVI-I Dual-Link Connector (DVI-I DL / DVI-D)) for the above setups are listed but this website has not been updated for years.
The currently most affordable NVIDIA 3D Vision solution on Linux (2013+ workaround) is to buy a monitor with built-in IR emitter (for example BenQ XL2420TX or ASUS VG278HR), and a cheap Quadro, e.g. the FX380 or K420. The latter has a Dual-Link DVI (DVI-D) and a Displayport outlet, so can drive the stereo monitor, and an additional monitor. This solution avoids the USB/3-pin hassle altogether. See below for xorg.conf! GeForce cards (instead of Quadro) do not give openGL Quad Buffered Stereo on Linux (on Windows neither).
The Nvidia page that names monitors with built-in emitter also has not changed for years. http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 3D-emitter" attribute. This currently only returns the Asus 278HR which can only be bought in Poland, or through EBay.
Cheap Quadros with DVI-I Dual-Link Connector (DVI-I DL / DVI-D) or DisplayPort work well. Make sure the card can do dual-link DVI if your monitor has only DVI-D input. Any card (including the "Windows only" ones!) listed should work if a) it can do dual-link DVI if the monitor has only DVI-D input, and b) if the monitor has built-in emitter. DisplayPort works well with the BenQ XL2420TX.
For Quadro with DisplayPorts 1.2 only, you will need a Club-3D CAC-1051 active DisplayPort/Dual-Link DVI Adapter 330MHz (110 €: do not buy the cheaper 270 MHz model, it will not work because the bandwidth is too low for 1920x1080@120hz) or for cards with miniDisplay ports, the Club-3D CAC-1151 active miniDisplayPort/Dual-Link DVI Adapter 330MHz.
specs of latest ("Maxwell") and previous ("Kepler") generation of Quadro cards are at http://www.nvidia.com/object/quadro-desktop-gpus.html . A comparison of all PCIexpress Quadro cards is at http://en.wikipedia.org/wiki/Nvidia_Quadro#PCI_Express . Latest (2014+) with prices are at http://www.heise.de/preisvergleich/?cat=gra16_512&asd=on&asuch=quadro&xf=3312_2014&sort=p . Currently (2015), the K620 is the entry system with the best price/performance ratio; in the middle range the K2200 still seems affordable.

Software

Linux

Zalman Stereo is supported by Coot; no drivers or other software must be installed.

NVidia 3D Vision 2: Using NVidia's 346.35 driver on RHEL/CentOS/SL 7, I changed /etc/X11/xorg.conf (see http://us.download.nvidia.com/XFree86/Linux-x86_64/346.35/README/xconfigoptions.html) to have

   Section "Device"
      Driver      "nvidia"
      Option      "Stereo" "10"
   EndSection

but there was no stereo (coot only shows a slightly rotated view), nor was there any hint in /var/log/Xorg.0.log that stereo is disabled. In fact, stereo is disabled, due to the Composite Extension (see http://us.download.nvidia.com/XFree86/Linux-x86_64/346.35/README/xcompositeextension.html). If this extension is itself disabled by

   Section "Extensions"
      Option     "Composite" "Disable"
   EndSection

then the login screen (gdm) crashes (discussed at https://devtalk.nvidia.com/default/topic/556113/3d-vision-and-composite-option). The only way out is to install a different display manager, like documented at e.g. http://jensd.be/?p=125 (confirmed by Dirk Kostrewa in 9/2014). This works well - I'm now using lightdm and the MATE desktop with a NVidia Quadro K420 and a BenQ XL2420TX. The graphics performance is very good for electron density inspection and fitting.

Mac OS X

The following command needs to be run for Macs to be able to support stereo in X11 programs, such as Coot [1] :

    defaults write com.apple.x11 enable_stereo -bool true

Ono

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) [2]

Stereo on conventional CRT monitors

Some of the NVidia 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 (difficult to find these days, around 450 €), 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"
   End Section

For an example of how else to configure xorg.conf, see old versions of this article.