I am building a complete new system (3D design workstation) but am not really sure where to start. I want a SLI/CrossFire compatible setup but want to only support companies which have open support so that I can use Linux or any other FOSS OS. What do people recommend?

By 'want to only support companies which have open support' what exactly do you mean?

Both nVidia and ATI/AMD GPUs have open soruce driver support. AMD/ATI has provided some documentation and developper time for teh opne soruce drivers. nVidia provides no support at all for the open soruce drivers. If you are going to be running a high performance workstation you will probably want to use the closed source drivers anyway. AMD/ATI fglrx and nVidia drivers support SLI/Crossfire.

Not that corssfire/SLI is worth it IMO, unless you want to spend a huge amount on video cards.

I'm buying a low / mid end video card as well. Is one of the drivers (AMD or nVidia) slightly better than the other? Just wondering?

IMO the nVidia close source drivers are better than the AMD/ATI closed drivers, and the AMD/ATI open source drivers are better than the nVidia open drivers.

3D workstation professional grade video is a whole different ball park. The contrast between AMD and nVidia has been made above and as cascade9 said, you'll probably want the closed source drivers for maximum feature set anyway whether you go Quaddro or FireGL.