What's the counselor recommendation letter?
In a traditional school, the counselor letter is a way for the high school to give the college an idea of what the student is really like, beyond the GPA and test scores. Often students can look almost identical on paper, so when a school counselor talks about how one student is always cheerful and helped a classmate get through their parents' divorce or how another student comes from a single-parent home and has to take care of his grandmother and younger siblings after school and hold down a part-time job on the weekends, it gives the colleges insight into that student's strengths, which allows them to select the students that would be the best fit for their school.
With homeschoolers, the basic idea is the same: you want to give the school an idea of what makes your child special, what sets them apart from the other applicants, and what makes them a good fit for the school (although your letter has to be general enough to apply to every school that takes the Common App). Since the schools know you're the parent and are going to be biased in your assessment, you need to give examples of how your child stands out. So you can say things like, "Johnny is always willing to help another student. For example, his CC prof/coach/co-op teacher asked him to help another struggling student after class, and he later told me that Johnny was the hardest working teen he'd worked with in years." Or "Janey has a knack with connecting with younger kids. In fact, she was offered a part-time job at her ballet studio to help with the younger dance classes."
Don't reiterate anything in your counselor letter that's listed in the application. This is your only opportunity to make your child a human in the admissions officers' eyes.
The only time you'd want to repeat something that's listed in the application is if the listing in the activities section doesn't give you enough space. For instance, if your child is is president of a club, that's great and it's listed in the activities and you shouldn't mention it in your letter. But if being president meant that they founded the club and made it competitive in one year, then that's something to discuss in the letter.
This is also a good place to mention things that happened before high school that were significant, such as doing well in a national competition, as long as those accomplishments illustrate one of your child's characteristics. Don't include anything that happened before high school unless it relates directly to their character--admissions officers aren't interested in things that happened four years ago. But if your child won second place in the national competition of National History Day or Young Scientist Challenge, mention it, as it demonstrates what a hard-working kid they are.
The idea is to give the admissions officers a way your kid can be an asset to the student body while giving them a glimpse into their human side.
Honestly, the counselor letter was the thing I struggled with the most in the whole application process, so good luck!