Can you restate slightly, email templates are sent 'out' from JIRA as part of an issue event notification, adding a Hyperlink that was 'user provided' could be as simple as modifying a template to include a specific custom field:
- https://developer.atlassian.com/display/JIRADEV/Adding+Custom+Fields+to+Email
If you want to provide that custom field value, through email, there are some plugins that can help. Working from JIRA out, you could use JEMH, a mail handler for JIRA 5.x, this allows intelligent processing of email content, allowing a remote user to supply that hyperlink via Directives in the email, eg:
--- body-starts ---
@Your Custom Field = http://www.google.com
This is the rest of the email
--- body-ends ---
If using JEMH, you can use JEMH to allow creation of custom templates rather than modifying JIRA .vm files, and changes can be made 'live' rather than requiring a JIRA restart.
There are other plugins that integrate with mail clients as well as having something on the server which may also work.
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