This is one of those \'oh my god\' moments.
The previous programmer in our company has left behind a badly-coded application using PHP and MySQL.
One example
You could use FIND_IN_SET to retrieve rows that match your criteria:
SELECT * FROM your_table WHERE FIND_IN_SET('value', field_with_comma_sep_values) > 0;
Basically, FIND_IN_SET
returns the index of the found item. So this query finds all rows where it finds the matching word in the "set" of comma separated values.
Credit: I knew there was something like this, but this post is where I found the answer and the SELECT statement.