I recently built a new PC and my video card will idle at around 29C, however when I play Battlefield 3 my CPUID HW Monitor has recorded maxes of 84C and 85C, but the fans only run at about 50% capacity. Should I be worried about this or is this perfectly safe, I've seen conflicting reports on a lot of different forums.
I am currently installing MSI afterburner to try and set the video card fans to run at a higher speed, but is there anything else I should/could do?
84 is quite warm, but not dangerously so. I would try a custom fan profile, cranking up the fans higher will definitely help. You may also want to check airflow into the case. If your card takes in air from below it, a side intake fan situated below the graphics card will provide more air to cool the graphics card.