Email templates can be created in either HTML or text formats.
Most email clients such as Outlook automatically create links for text format emails. However, HTML emails must have the link defined in the email.
Here are the steps to ensure links are displayed correctly in an HTML email template:
1. Edit the HTML email template:
Setup | Communication Templates | Email Templates,
Click the Name of the Template then click "Edit HTML Version".
2. Enter the text that you would like to be hyperlinked
3. Highlight the text of the link and click the "Insert a link" icon
4. Paste the merge field
(for example : "!Opportunity.Customer_Payment_URL__c} ") on the URL window or any other URL you need and then click OK
5. Save the template
Links from this HTML email template will now be clickable from Outlook or other email clients.