My system specs are not near as high as yours (see below), but I was able to cure ALL the skipping/hesitation in both HL2 & Far Cry.
I thought my system wasn't quite high enough to run the games with everything maxed out at 1280x1024 (LCD monitor limits), but I was wrong.
My 6600GT runs a little O/C'd @ 550mhz core/1.1gig memory. Thought maybe with the 128mb of memory both games were running out of GPU memory and was fetching more needed memory from system (I don't really know how PCIe does it vs AGP).
I thoroughly cured both games by going from 512mb to 1.5gig of DDR2 system RAM! Where I was running HL2 at medium settings @ 1280x1024 with frequent stuttering I know run with everything set to high with NO stuttering whatsoever. Far Cry was similar in that I had to run @ 1024x768 with most settings at medium. Now runs 1280x1024 with all settings set to VERY HIGH. The only rare stuttering I run into is when my weapon fires and it makes a muzzle flash, but only a split second vs several seconds with 512mb.
Try to borrow another stick of 512mb or 1gig memory to slap in your system to see if you get the results I got. With an AMD 64 & 6800GT you should easily run much smoother than mine.