I feel your pain. I just put together an Asus Sli Premium W\ AMD 4000+ and an Asus 7800GTX. I am running a single card at present. I was really chopfallen to see the sluggish frame rates in HL2 (especially split second freezes just prior to explosions, it reminded me of Half Life on my P166 ).
The fix? Asus A8N motherboards are still coming with the 1008 bios. Update to the 1009 bios (if you're really feeling brave you can try the beta, but I would wait). All I can say is this is what made a big difference for me. Damn smooth now. I'm not finished messing with this thing though. I think there's alot to be found yet but I want everything to be running smooth and stable at "stock" settings before I start messing 'inside' the bios or with the graphics card (still looking for the VGA bios). So far I'm not that impressed with the nvidia NF4 chipset but I have hope.
Use the Asus Update tool. Download the appropriate motherboard bios to a folder and direct the update tool to there to flash. Don't bother trying to get the tool to download the bios itself. Other than that it's fool proof. Don't be intimidated by it.
Once again, I think it's very important that you have all the latest drivers from Asus or nVidia (chipset, graphics etc...) and an updated bios before you start messing with anything else. You shouldn't have to be resorting to tweaks to get HL2, definitely HL2, to run smooth at it's default settings. Now a game like F.E.A.R. is antoher matter, that could bog down the best of rigs.
Good luck!