If you have chosen WMV9 to encode and your encoding takes a long time, you will not be able to do other tasks in your PC as faster as you were able to. The reason is your CPU usage is 100% while the video is encoding.
With a HTT enabled PC you have the flexibility in choosing either both processors or one processor for encoding.
Go to Windows Task Manager
Go to Proceses tab
Locate wmenc.exe and right click
Click Set Affinity...
Deselect one of the CPU and press OK
Your CPU usage will lower down to around 50%
You will now be able to continue your other light work while WME is doing its encoding
I guess that WME is not fully optimized for Hyper Threading Technology yet, since I didn't notice any degrade in encoding speeds aftwarwards