Is there anyway to scan Lotus Notes application database and find out the applicaitons that send e-mail to the users?
You can do a script analysis in MNSP and find out where certain functions or formulas (e.g. @MailSend) are present. However you will not be able to find out with MNSP if these are actually used - often they are part of a script library or element but not enabled. Up to a point Notes Designer can help you, of course. For advanced source code / design analysis I would recommend something like www.teamstudio.com/analyzer.
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