Użyj:
SELECT tm.*,
x.listcount,
y.uploadcount
FROM $tbl_members tm
LEFT JOIN (SELECT tl.username,
COUNT(tl.listname) AS listcount
FROM $tbl_list tl
GROUP BY tl.username) x ON x.username = tm.username
LEFT JOIN (SELECT tu.username,
COUNT(tu.id) AS uploadcount
FROM $tbl_uploads tu
GROUP BY tu.username) y ON y.username = tm.username
GROUP BY tm.username
ORDER BY tm.lastname, tm.firstname