For HD videos in the best quality with the best compression:
Destination: Make sure you set the file format as MKV.
Size: Original (auto-set)
Modulus: 2 (default)
Filters: All off.
De-interlace: Only if using a US file in a Non-US device (Better to turn it off and set this in the video player.)
x264 preset: Set this to the slowest possible setting your PC and patience can handle. Slower = higher quality & smaller files.
Video Codec: H.264 (x264)
Framerate: Same as source. (NTFS (USA) = 29.97 fps, PAL(Worldwide) = 24/25 fps.)
Leave the rest on default.
Codec: MP3 or AAC. For best compatibility, pick MP3. Most videoplayers have cut out AC3 and DTS support due to licensing issues. (And Stock never supported DTS anyway.) AAC is also an option.
Bitrate: For best sound quality, 192 and above.
Sample Rate: Auto.
Mixdown: Depends on what's originally included in the file. You can't force a 2:1 onto a 5:1. (The audio track should say what it is.) If unsure, use default.
DRC: Leave alone
Gain: If you find the sound too quiet, add 1-5 points.
If you've got a .srt file you want to bake into the video file, add here. If you prefer to use a separate .srt file (same name as the video = auto detect by most players), skip.
If you want to make chapters, do so here. If not, skip.
Don't know if Stock plays MKV, but you're better off using another app anyway. VLC, Dice, MXplayer, BSplayer. Any of those.