Intente esta consulta a continuación. Usando ROW_NUMBER() OVER(PARTITION BY ..)
generar un rango/número de registro para cada 'which'
elementos y ordenar en base a esto. (Espero que esto funcione para usted, no tengo el esquema de tabla o el script de datos de muestra para probarlo yo mismo)
SELECT
pr1.id AS user_id,
pr1.title AS user_name,
pr2.id AS liker_id,
pr2.title AS liker_name,
x.which AS which_table,
x.cnt AS total
FROM
(
SELECT rid, rootid, which, COUNT(*) AS cnt
,ROW_NUMBER() OVER(PARTITION BY which ORDER BY rid) AS new_order
FROM
(
SELECT rid, rootid, 'vote' which FROM p_likes
UNION ALL
SELECT rid, rootid, 'comment' which FROM p_comments
UNION ALL
SELECT rid, rootid, 'friend' which FROM relations
) y
WHERE y.rootid = 1246 AND y.rootid <> y.rid
GROUP BY y.rid, y.rootid, y.which
) x
INNER JOIN pagesroot pr1 on x.rootid = pr1.id
INNER JOIN pagesroot pr2 on x.rid = pr2.id
ORDER BY new_order,x.cnt desc;