Try this
SELECT [September 2012 Billing File] =
CASE
WHEN T2.[Application ID] IS NOT NULL
AND T2.[ServerName] IS NOT NULL
AND SUM([Billed This Month]) <> 0
THEN 'Y'
ELSE 'N'
END
FROM[AEG_DB].[dbo].[TBL_Work] T1
LEFT JOIN[TBL_Data] T2
ON (T1.[Application ID] = T2.[Application ID]
AND T1.[ServerName] = T2.[ServerName])
WHERET2.[Data Period] = 'September 2012'
GROUP BYT2.[Application ID],
T2.[ServerName];
