Vace,
For some reason I didn't get notification about your reply until yesterday...
Anyway the Affinty mask tells WoW how many layers or masks it will spread across your CPU's. Some people notice that WoW will use all available cores, but one more than others, and cause FPS issues.
Again I don't know all the technical mumbo jumbo behind it, but it works. If you add it though, be careful as sometime it will remove it. I have seen issues where WoW doesn't truly detect the mulitple cores on the E6600ish family, but usually a clean install of the game will correct that.
The autotuning is something Microsoft implemented in Vista to help "speed" up network processes but it just causes more pain than its worth.
I have been running good now though for a while. Got the guild's first peice of Ulduar loot last night WOOT.
Just for reference I am currently using:
Asus P5N32-E SLI Plus
Q6600 non-OC (board has issues with it)
BFG GTX 260
OCZ Reaper DDR2 1066 8GB
2x GSKILL 64 GB SSD in Raid
I still get 30ish FPS in Dal, but the SSD upgrade recently is insane, from Character Screen to fully loaded in Dal in 8 seconds.