gis=# explain analyze
SELECT
  AsText("way") AS geom,
  "ref"
from (
  select
    way,
    array_to_string(array(select * from unnest(array_agg(ref)) order by 1), ', ') as ref
  from (
     select distinct on (w.way,ref)
       unnest(string_to_array(r.ref, ';')) as ref,
       w.way as way
     from
       planet_osm_line w, planet_osm_line r
     where
       (r.route='train' or r.route='railway' or r.line='rail')
       and (w.osm_id > 0) and (r.osm_id < 0)
       and ST_Within(w.way,r.way)
    ) lines
    group by way
  ) as routes
WHERE "way" && SetSRID('BOX3D(-6506931.343860455 -4139217.955698919,-6495924.411787389 -4128211.023625853)'::box3d, 900913);