SQL Server has a utility used by replication to compare data in two tables for non-convergence. This utility can be called from the command prompt or in a batch file. Look here for details: http://msdn.microsoft.com/en-us/library/ms162843.aspx.
I used this utility to find differences between tables located on two different servers. This gave me very fast output.
An example bat file is as follows:
cd "c:\program files\microsoft sql server\90\com"
tablediff -sourceserver "[SourceServer]" -sourcedatabase
"[SourceDatabase]" -sourcetable "[SourceTable]" -destinationserver
"[DestinationServer]" -destinationdatabase "[DestinationDatabase]" -
destinationtable "[DestinationTable]"
pause
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