Previously I wrote on how to manually encode ProRes on Windows. The process I detailed, while effective, can be cumbersome and intimidating, especially to those with little knowledge of command line operations within Windows.
In the article, I also mentioned Cinec which does the process automatically. Since writing, however, Cinec has changed their free product to pay in violation of the ffmpeg license terms that the product is based upon (GNU GPL v2.1).
Fortunately, there exists a truly free and open source option thanks to the developers of the also free and open source NLE Lightworks. Eyeframe Converter is a batch processor for encoding to a number of formats. It's built off ffmpeg as well and even allows you to add aditional custom presets based on ffmpeg commands.
The software (which can be downloaded here) has options for ProRes HQ and 4444 and requires no command line interaction. You merely drag your clips into the software, click convert and then select either
LW PRO ProRes HQ + Embed TC & RN - Proxy (for ProRes 422 HQ) or
LW PRO ProRes 444 HQ + Embed TC & RN - Proxy (for ProRes 4444). You chose the destination folder, select okay, and you're rendering. I oftentimes encounter a bug where I get a dialog box upon the completetion of rendering that reads "Failed to convert," but the converted clips are always there and play across Win/OSX/*nix and in all software I've encountered.