Stereo

Hardware

Zalman Stereo

has its own article.

Nvidia 3D Vision 2

3D Vision Pro is not what you want, this seems to be for projectors, and is expensive.
Quality of Nvidia 3D Vision is better than that of Zalman
Compatible monitors are mentioned at www.nvidia.com/object/3d-vision-displays.html but this website does not seem to be updated. There are 5 monitors (needing a separate emitter) at http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=3135_passiv#xf_top .
The Nvidia 3D vision emitter that connects via USB only works on Windows, not Linux. Linux needs the DIN 3-pin connector which is only on the high end Quadro cards.
The currently (2013+) best NVIDIA 3D Vision 2 solution on Linux is to buy one of the monitors with built-in emitter (we have the BenQ XL2420TX), and a cheap Quadro, e.g. (2013) the FX380 or (2015) K420. The latter has a Dual-Link DVI 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! We found that using a GeForce card instead of Quadro does not work on Linux.
www.nvidia.com/object/3d-vision-displays.html names monitors with built-in emitter. None of these are sold any more in Germany or the EU, it seems - the NVidia page has not changed for at least the last two years. But: As of January 20, 2015 http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=3135_3D-f%E4hig%7E3135_aktiv#xf_top shows 8 3D-capable monitors with built-in emitter; ASUS VG248QE and VG287HE and VG278HR, Acer GN246HL and Predator XB240HAbpr and HS244HQbmii, BenQ XL2430T, Philips 273G3DHSB. All of these are 24-27" and cost between 205 and 490€.
cheap Quadro cards with dual-link DVI-D or DisplayPort work well. Quadro 380, 400, 420 and 600 have been reported to work on CCP4BB. Make sure the card can do dual-link DVI if your monitor has only DVI input. Any card (including the "Windows only" ones!) listed at http://www.nvidia.com/object/3d-vision-pro-requirements.html#Quadro should work if a) it can do dual-link DVI if the monitor has only DVI input, and b) if the monitor has built-in emitter. DisplayPort is fine with the BenQ XL2420TX.
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.