After a recent update, the Opportunity.Link field* started containing only the SalesForce ID in one of my email templates. In the past, this contained a full and valid URL.
Due to the standard support response time, I created a formula field called Link with an API name of Link__c and had it create a URL that was valid in production for my instance. This allowed my users to have a valid link in their emails and things were going fine.
Tier 2 support told me the issue had been resolved but when we tested it in the sandbox, the standard link field now contained a valid URL but it pointed to production instance server.
After reaching tier 3 support, I was told that my custom field was causing the issue as it was to similarly named. With much skepticism, I renamed my custom field and re-tested. Sure enough this corrected the issue and support was right.
This is very odd behavior given that the email template was using the API name and not the field name or field label.
Anyway, 2 thumbs up to support for running this down.
* I put a star by this because it isn't actually a field you can query via SOQL - at least not in force.com explorer.