Your best option will be to use ffmpeg. It’s a command-line tool, but don’t let it put you off, it’s fairly simple to use once you get the hang of it — spend an hour or two reading through the manual, take a few notes on the most common flags/commands for your work, and you’ll be fine. It gives you far far more control and power than other tools, even tools like Sorenson, and it’s really easy to automate for handling entire folders and oft-repeated jobs (just make one batch file to transcode your dailies folder and run it on a 12 hour interval, bam, never think about it again).
It’s also the only tool available that can can encode ProRes on Windows.