Demystifying HandBrake’s settings

Handbrake is an incredibly useful piece of software, but also pretty intimidating because of it’s multitude of customizable options. Most people, including myself, gloss over when things like MP4 ,MPEG-4, FFmpeg, XviD, H.264, AAC, AC3, Dolby Pro Logic II, 6-channel Discrete, 2-pass encoding, Turbo First Pass option, MKV, AVI, etc. I’ve read a few different articles in the last few years about the numerous options, but none compare to this one.