raising agp speed can be dangerous, but the magnitude depends entirely on what architecture of card you're using. some bus oc much better, and some benefit more from it.
my 5900xt is running at a full 99MHz agp (and 5950u speeds) 100% stable, and has been for a long time now. 3dmark03 game 2 was choppy until I moved the bus above 75. so yeah, it can make a difference... I don't know about your card because of the amount of processing power a 6800 GT has and a lack of experience with that card, I don't know how much it will help or how flexible the card is to bus oc.
you have an NF3 mobo. by default NF3 boards (like NF2) have an individually locked pci bus. you don't have to bus oc your pci to bump the agp. if no pci setting is displayed in the bios, it is probably defaulted to the standard 33. you shouldn't have to worry about agp bus oc messing up your pci hardware.
bottom line: don't be too afraid to try bus oc, but don't take it too far unless you're prepared for the possible consequences. just like any other oc.
oh, and don't be shocked if you don't see a 300 point boost in and 3dmark after moving past 75MHz.
