Yeah, play around with the X264 settings and some of the filters, and remember that you can save your own profiles to use as a starting point later. A lot of guides try to use the settings to target specific players, but I did the opposite. I picked settings to get the highest possible quality out of the source material. For example, I have SD and HD versions of profiles for "live TV", "animated TV", "live film", "animated film", and even some with default subtitle support. Some settings work great for animation but are totally inappropriate for live action video. Experiment and save your settings. Deinterlacing or decombing (or detelecining) is appropriate for television, but will hurt most movies.

https://trac.handbrake.fr/wiki/CLIGuide is a good resource.