Hi @jonb,
The short answer is yes, it is possible, but generally not recommended.
For example, you can launch the entire desktop environment via VirtualGL by setting the relevant cmdline parameter in profiles.hconf to something like vglrun +wm mate-session (or whatever your desktop environment happens to be).
But this means every single application will be run through VirtualGL’s interposer (including the desktop environment itself). This makes life easier for the end user, but isn’t very efficient use of system resources.
A common approach is for administrators to create application shortcuts which launch via vglrun. If you are using a desktop environment which confirms to freedesktop.org standards (such as MATE or Xfce), the ThinLinc Desktop Customizer can be used to manage these shortcuts:
For more information on using VirtualGL in ThinLinc, see:
Hope that helps!