We have a VB application which automatically sends an email to Exchange distribution group and Outlook is flagging that mail as "Potentially Unsafe" (Red warning on top of the mail). VB application is sending those mails using our exchange SMTP port. The mail has HTTP links. Is there any method I can add these type of mails to a whitelist? Thanks.

Depending on what is on that message you can configure different options as per KB You may receive an "Outlook blocked access to the following potentially unsafe attachments" message in OutlookSukh

The mail does not have any attachments. Few lines of text and couple of hyper-links. The warning header does not say anything about attachments. It says "The mail is potentially unsafe and links have been disabled". I will try to post a pic if I can. The actual hyper-links in the mail work fine despite Outlook saying it disabled links.

Can you check these settings here Enable or disable links and functionality in phishing e-mailSukh

The link you have posted explains what my clients are facing. I can remove the warning by placing the sender in "Safe senders list" but I am wondering if there is any server side solution (not Group Policy) to do this. We are planning to introduce more applications which send mail automatically. The "from" email address in the VB Application is our Exchange internal mailbox name and I am assuming it is considering it as phishing attack as we are sending it through SMTP port.

Not a native solution, if you're using Exch 2007/2010, you can try to mark the email with an SCL rating of -1 using a transport rule.Sukh