WHERE [...] players.player_id IN (SELECT retournant IDs des joueurs du classement général)

SELECT clans.clan_tag, clans.clan_id, SUM(scores.played_time) AS played_time, SUM(scores.frags) AS frags,
  SUM(scores.gibs) AS gibs, SUM(scores.teamkills) AS teamkills, SUM(scores.teamgibs) AS teamgibs, SUM(scores.suicides) AS suicides,
 SUM(scores.deaths) AS deaths, SUM(scores.ctfscore) AS ctfscore, SUM(scores.htfscore) AS htfscore, 
SUM(scores.ktfscore) AS ktfscore, SUM(scores.RETURN) AS `return`, SUM(scores.steal) AS steal, SUM(scores.points) AS points
FROM scores
INNER JOIN players ON scores.player_id = players.player_id
LEFT JOIN clans ON players.player_clan = clans.clan_id
WHERE scores.date LIKE '$date' AND players.player_clan GROUP BY clans.clan_id
HAVING SUM(scores.points) >= 1000 AND SUM(scores.played_time) > 3600
ORDER BY SUM(points)/SUM(played_time)
DESC LIMIT 50

SELECT p.player_id, p.player_clan, sum(s.points) points, sum(s.played_time) time, etc.
FROM players p
INNER JOIN scores s ON s.player_id = p.player_id
HAVING sum(s.points) >= 1000 AND sum(s.played_time) > 3600
GROUP BY p.player_id, p.player_clan

SELECT c.clan_tag, c.clan_id, sum(j.time) played_time, etc.
FROM clans c
INNER JOIN (
  SELECT p.player_id, p.player_clan, sum(s.points) points, sum(s.played_time) time, etc.
  FROM players p
  INNER JOIN scores s ON s.player_id = p.player_id
  HAVING sum(s.points) >= 1000 AND sum(s.played_time) > 3600
  GROUP BY p.player_id, p.player_clan
) j ON j.player_clan = c.clan_id
GROUP BY c.clan_tag, c.clan_id
ORDER BY sum(j.points) / sum(j.time) DESC
LIMIT 1, 50