best way for creating Index in mysql (multi-column/table)?
See if this runs faster:

SELECT  n.ID, n.LATITUDE, n.LONGITUDE,
        wn.WAYID
    FROM  
      ( SELECT  ID, LATITUDE, LONGITUDE
            FROM  `node`
            WHERE  LATITUDE  BETWEEN '49.558'  AND '49.568'
              AND  LONGITUDE BETWEEN '11.3395' AND '11.3495' 
      ) AS n
    JOIN  `waynode` AS wn  ON n.ID= wn.NODEID
    ORDER BY  wn.WAYID 


This might also work 'fast':

SELECT  n.ID, n.LATITUDE, n.LONGITUDE, 
      ( SELECT  WAYID
            FROM  waynode
            WHERE  n.ID= NODEID 
      ) AS WayID
    FROM  `node` AS n
    WHERE  LATITUDE  BETWEEN  '49.558' AND '49.568'
      AND  LONGITUDE BETWEEN '11.3395' AND '11.3495'
    ORDER BY  WayID 


For further discussion, please provide EXPLAIN SELECT ... for any query you want to discuss and SHOW CREATE TABLE ... for the tables in question.