Following DeHackEd's example, I started writing a PowerShell script to help automate the encoding process. After some time, I made v1 which is a jumbled, barely-working mess, however it works well enough for me:
http://ccfreak2k.loliserv.org/nesencodingv1.zip
The script is under the BSD license
It's written in PowerShell (as said earlier), so you'll need to have that installed to use it (if you intend to). Just drop the script, along with mencoder.exe and the config file, in some directory, edit the config file to your needs, then run the script. After a while, the video will be done encoding. mencoder.exe will drop its standard output to the console. In addition, headers will fly by before each step, the window title bar will also print the step, and it will stop and tell you which step had an error with which error code.
Missing but potentially useful features:
*The ability to arbitrarily pick which step(s) to run.
Like I said, the script works well enough for my needs. I'm just sharing it in case someone else might find it useful. However, I spent a great deal of time and effort building debug information into the script to help diagnose errors. If you encounter any PowerShell interpreter problems (
red text), be sure to tell me about it.
Trendline added at DK64_MASTER's request.
This helped for me. Anyone else wanna confirm?
EDIT: I also tested it using the Hacktarux wrapper linked above, and it 
