Try this:
Select Top 1000000 tblSoftwareUni.softwareName As Software,
tblSoftware.softwareVersion As Version,
tblSoftwareUni.SoftwarePublisher As Publisher,
Count(tblSoftware.AssetID) As Total
From tblSoftware
Inner Join tblAssets On tblSoftware.AssetID = tblAssets.AssetID
Inner Join tblSoftwareUni On tblSoftware.softID = tblSoftwareUni.SoftID
Inner Join tblAssetCustom On tblAssets.AssetID = tblAssetCustom.AssetID
Inner Join tblAssetGroupLink On tblAssets.AssetID = tblAssetGroupLink.AssetID
Inner Join tblAssetGroups On tblAssetGroups.AssetGroupID = tblAssetGroupLink.AssetGroupID
where tblAssetGroups.AssetGroup = 'Critical Systems'
Group By tblSoftwareUni.softwareName,
tblSoftware.softwareVersion,
tblSoftwareUni.SoftwarePublisher
Order By Total Desc