Passthrough graphics acceleration without extra command

Also this:

I suspect that you could write some kind of wrapper that will prepend all your commands with vglrun, but that would be quite annoying to handle. What if you need to run command without it?

I think the simplest way would be to just edit your desktop files. For instance, replace command in qubes-run-terminal for xfce4-terminal -x '/bin/vglrun bash'. This way you get vglrun shell when you start your terminal, and all applications that you run in it will have the same properties.

Similarly, you can edit desktop files for all applications that you want to be accelerated.