Consultar varias tablas con relaciones complejas

Esto debería hacer lo que quieras:

WITH a AS (
  SELECT item.id, string_agg(prefered_store.store::varchar, ',') wishlist_stores
  FROM item, list_wishlist, wishlist, prefered_store
  WHERE item.list=list_wishlist.list
    AND list_wishlist.wishlist=wishlist.id
    AND wishlist.prefered_stores=prefered_store.id
  GROUP BY item.id
), b AS (
  SELECT item.id, 
    string_agg(
      prefered_store.store::varchar || ',' || prefered_store.comment,
      ' ; ') item_stores_comments
    FROM item, prefered_store
    WHERE item.prefered_stores=prefered_store.id
    GROUP BY item.id
)
SELECT a.id,item_stores_comments,wishlist_stores 
FROM a,b
WHERE a.id=b.id