- A lightly shaded diamond is a regular earned run.
- A dark shaded diamond is a home run.
- A gradient-shaded diamond (dark near the edges and light in the center) is an unearned run.
I've never heard of that being a generally-accepted norm for paper scorekeeping, but it's a neat little undocumented feature in iScore-generated scorecards.
For the most accurate results, you'd need to have advanced scorekeeping turned on in the options and remember to carefully answer the question, "If the error hadn't occurred, would the runner have been out?" every time it appears. (Also don't forget to "Assign Error" for dropped foul-outs.) If you do that, iScore is pretty solid at figuring out what can otherwise be a very complex game reconstruction exercise in some situations, and the scorecard shading can help you figure out which runs were counted toward the ER pitching stat (and resolve any disagreements with a paper scorekeeper).