I see a few problems in your query.

1. Since you use LEFT JOIN with HistItems, you want to move condition on the Items table into the JOIN. See this blog post for explanations

http://beyondrelational.com/modules/2/blogs/78/posts/11135/why-left-join-doesnt-bring-all-records-from-the-left-table.aspx

2. Don't use DATEPART function for the year condition. Instead construct 2 dates for beginning of the year and beginning of the next year and use

myDateColumn >=@StartDate and myDateColumn < @EndDate

condition.

See this blog post for details

Bad habits to kick : mis-handling date / range queries


>This is now my final version with Pivot. At first I was reluctant to dive into Pivot but in hindsight it's easier than I expected. The result is exactly what I need:
>

>SELECT Ministerie, Departement, KSC, Kostensoort,
>		Year,
>		ISNULL(QPivot.[1],0.00) + 
>		ISNULL(QPivot.[2],0.00) + 
>		ISNULL(QPivot.[3],0.00) + 
>		ISNULL(QPivot.[4],0.00) AS Total, 
>
>		ISNULL(QPivot.[1],0.00) AS Q1,
>		ISNULL(QPivot.[2],0.00) AS Q2,
>		ISNULL(QPivot.[3],0.00) AS Q3,
>		ISNULL(QPivot.[4],0.00) AS Q4
>		
>FROM (SELECT DepGroups.dgName AS Ministerie,
>		Departments.deName AS Departement,
>		GLSub.gsAccount AS KSC,
>		GLSub.gsDescr AS Kostensoort,
>		DATEPART(YEAR,Runs.ruStartDat) AS Year,
>		DATEPART(Quarter, Runs.ruStartDat) AS Quarter,
>		SUM(itAmount) AS itAmount
>
>	FROM PayEmps
>	
>	JOIN Departments
>	ON Departments.DeKey = PayEmps.paDeKey
>	JOIN DepGroups
>	ON Departments.deDgKey = DepGroups.dgKey
>	JOIN Runs
>	ON Runs.ruKey = PayEmps.paRuKey
>
>	LEFT JOIN HistItems Items
>	ON Items.itRuKey = Runs.ruKey
>	AND Items.itEmKey = PayEmps.paEmKey
>
>	LEFT JOIN GLSub
>	ON Items.itGsKey = GLSub.gsKey
>
>	WHERE PayEmps.delFlag = 0
>			AND Runs.DelFlag = 0
>			AND Runs.ruConcept = 0
>			AND Runs.ruStatus = 5
>			AND DATEPART(YEAR,Runs.ruStartDat) = ?pnYear
>			AND Items.DelFlag = 0
>		        AND GsAccount = '4101'
>                        AND Runs.ruYear = 2015
>
>	GROUP BY DepGroups.dgName, Departments.deName, 
>		GLSub.gsAccount, GLSub.gsDescr,
>		DATEPART(YEAR,Runs.ruStartDat),
>		DATEPART(QUARTER,Runs.ruStartDat)) AS QuarterlyData
>	
>	PIVOT(SUM([itAmount])   
>        FOR QUARTER IN ([1],[2],[3],[4])) AS QPivot
>
>	ORDER BY Ministerie, Departement, KSC
>