!!! Ignore this, correction below
As far as I can see, grouping by the AD Department attribute is not possible as LS does not store it anywhere for computers. It is stored for users, but that doesn't help us here. It is rather easy to do by OU. Consider the following:
SELECT
softwareName AS [Software]
,OU AS [OU]
,COUNT(*) AS [Installed]
FROM tblSoftware
LEFT JOIN tblADComputers
ON tblSoftware.Computername = tblADComputers.Computername
WHERE
softwareName LIKE 'Microsoft Office%'
AND softwareName NOT LIKE '%Communications Server%'
AND softwareName NOT LIKE '%Live Meeting%'
AND softwareName NOT LIKE '%Viewer%'
AND softwareName NOT LIKE '%Communicator%'
AND softwareName NOT LIKE '%Web Components%'
AND softwareName NOT LIKE '%Resource Kit%'
GROUP BY softwareName, OU
ORDER BY SoftwareName, OU