How to redirect links in email template to salesforce1 app

You can place links in email templates that navigate to the Salesforce1 app in the following format:

com.salesforce.salesforce1://entity/view?entityId={Account.Id}

I suggest you put that in alongside the standard {Account.Link} and give users a choice.

e.g.

To view this record please select either: {Account.Link} to view this in your browser com.salesforce.salesforce1://entity/view?entityId={Account.Id} to open in Salesforce1*