A Query with a Dynamic Case clause or how to avoid Case When
Not sure what reporting question you are trying to solve, but it looks like you can get what you're after by simply referencing the joined column. Here's a couple examples:
/* Count of certifications held by all employees */
SELECT  c.name
        ,COUNT(1) AS certCount
FROM    qualification AS q
        INNER JOIN certification AS c ON c.id = q.certificationid
GROUP BY
        c.name;

/* Count of certifications held, grouped by employee */
SELECT  q.employeeid
        ,c.name
        ,COUNT(1) AS certCount
FROM    qualification q
        INNER JOIN certification AS c ON c.id = q.certificationid
GROUP BY
        q.employee_id
        ,c.name;