DECLARE @Year int
SET @Year = (Select datepart(year,getdate()))

SELECT		dt.IDCode, intWeek, intYear, dt.KeyFigure
FROM
(
SELECT		Y.IDCode ,
			intWeek, intYear,
			KeyFigure = (SELECT count(coID) FROM TableB B
										INNER JOIN TableC C ON C.Date = DATEADD(dd, 0, DATEDIFF(dd, 0, B.inputDate))
										INNER JOIN TableR R ON R.IDCode = B.IDCode
										WHERE C.intYear = H.intYear
										AND C.intWeek = H.intWeek
										AND	C.Calender = 'FirstCalender'
										AND	(typ = 'pppp' OR typ = 'llll')
										AND	R.Des = 'SomeStuff'
										AND	((@Site IS NULL) OR (B.Site = @Site))
										AND Cat  = 'SomeCategory' 
										and El = 'sdhsjhjh' 
										and Sub IN ('2', '4', '43', '1', '99', '123'))
FROM		TableY Y
INNER JOIN	TableG G On G.gID = Y.IDCode
INNER JOIN	TableH H ON H.Dates = DATEADD(dd, 0, DATEDIFF(dd, 0, Y.inputDate)
WHERE		G.gMat = 'xxx'
AND			H.Calender = 'FirstCalender'
AND			(typ = 'pppp' OR typ = 'llll')
AND			(H.intYear = @Year or H.intYear = (@Year -1 ))
)dt 
GROUP BY	dt.intYear,dt.intWeek, dt.IDCode, dt.KeyFigure

SELECT columns...
FROM
(
--The below is your current query
SELECT ROW_NUMBER() OVER (PARTITION BY YourPeriodColumn ORDER BY KeyValue DESC) AS Rn,your other columns...
FROM...
)t
WHERE Rn<=5