Using an alias in a window function in a query in PostgreSQL

wrap the windowing in a surrounding query:

SELECT salary, result OVER (ORDER BY result)
FROM (SELECT salary, (...expression...) AS result
      FROM empsalary
     ) x

Place the alias behind the OVER clause:

SELECT salary
     , sum(salary) OVER (ORDER BY salary) AS my_alias
FROM   empsalary;

Edit after question update

You cannot reference a column alias (an "output column") at the same level of a SELECT. You need a subselect or a CTE for this. Like:

SELECT id, result, rank() OVER (ORDER BY result) AS rnk
FROM  (
    SELECT id, <complex expression> AS result
    FROM   tbl
    WHERE  <some condition>
    GROUP  BY id
    ) sub;

For your query:

SELECT rank() OVER (ORDER BY deltahdlcOverruns) AS rnk
     , y1_
     , deltahdlcOverruns
FROM  (
    SELECT this_.deviceNo as y1_
        ,  (SELECT _dev_.hdlcOverruns FROM abstractperformancestatistic _abs_ 
            JOIN   enddevicestatistic _dev_ USING (id)
            JOIN   linkstatistic _link_ ON _link_.id = _dev_.linkStatistic_id 
            JOIN   iptstatistic _ipt_ ON _ipt_.id = _link_.iptStat_id 
            WHERE  this_.deviceNo=_dev_.deviceNo
            AND    _abs_.dateTime <= '3910-06-07 00:00:00.0'
            ORDER  BY _abs_.dateTime DESC
            LIMIT  1
           ) 
           - 
           (SELECT _dev_.hdlcOverruns FROM abstractperformancestatistic _abs_ 
            JOIN   enddevicestatistic _dev_ USING (id)
            JOIN   linkstatistic _link_ ON _link_.id = _dev_.linkStatistic_id 
            JOIN   iptstatistic _ipt_ ON _ipt_.id = _link_.iptStat_id 
            WHERE  this_.deviceNo=_dev_.deviceNo
            AND    _abs_.dateTime >= '3870-06-01 00:00:00.0' 
            ORDER  BY _abs_.dateTime
            LIMIT  1
           ) AS deltahdlcOverruns
    FROM   EndDeviceStatistic this_ 
    JOIN   AbstractPerformanceStatistic this_1_ USING (id)
    JOIN   AbstractEntity this_2_ USING (id)
    LEFT   JOIN RawEndDeviceStatistic this_3_ USING (id)
    LEFT   JOIN LinkStatistic l2_ ON this_.linkStatistic_id = l2_.id 
    LEFT   JOIN AbstractPerformanceStatistic l2_1_ ON l2_.id = l2_1_.id 
    LEFT   JOIN AbstractEntity l2_2_ ON l2_.id = l2_2_.id 
    LEFT   JOIN RawLinkStatistic l2_3_ ON l2_.id = l2_3_.id 
    LEFT   JOIN IPTStatistic i1_ ON l2_.iptStat_id = i1_.id 
    LEFT   JOIN AbstractPerformanceStatistic i1_1_ ON i1_.id = i1_1_.id 
    LEFT   JOIN AbstractEntity i1_2_ ON i1_.id = i1_2_.id 
    LEFT   JOIN RawIPTStatistic i1_3_ ON i1_.id = i1_3_.id 
    WHERE  this_1_.dateTime between ? and ? 
    GROUP  BY this_.deviceNo
    LIMIT  ?
) x;

I made a few additional syntax simplifications.