I the Gospel Library app there are 10 colors. Each of these colors can be used in the underline, highlight, or text color mode.
I asked extended family what they do and one of my niece's responded with this color code:
- Red- doctrine
- Orange- clarifications or explanations of doctrine
- Yellow- commandments and specific instructions
- Purple- promised blessings and how to attain them
- Grey- power phrases
- Blue- favorites
- Dark blue- ones with a deeper meaning (I always attach a note with a dark blue)
- Pink- examples of Gods love/charity
- Brown-specific for our day
- Green - Not used

Here is also a color code based on the Seminary Doctrinal Mastery

My color code has evolved over the years. I used to mark my scriptures much more colorfully than I do now. When I picked up a new copy of the 2013 LDS Scriptures and started transferring some of my highlights I found my self doing less bold and fewer colored highlights. I pretty much use a red pencil to underline in my paper scriptures with an occasional yellow highlight.
After a bit of thinking, comparing, and pondering I decided to use the color code below for my electronic marking.
- Yellow - General highlights
- Red - Love, Charity
- Purple - Priesthood
- Orange - Atonement of Christ, Resurrection
- Green - Promised Land, geography
- Gray - The devil, Satan, darkness
- Pink - Pride