Incorrect Url in Email - WSSv3 / MOSS 2007

In WSSv3 / MOSS 2007 Reminder takes the hyperlink from the Default Zone set in Alternate Access Mappings

Click Start > Administraive Tools > SharePoint 3.0 Central Administration then select Operations
Under Global Configuration select Alternate Access Mappings
Select your website from the Alternate Access Mapping Collection drop down. If the URL you want to use in your emails is not the Default Zone then change the settings around. For example it is common for the computes NetBios name to be Default and the FQDN to be Intranet - these can simply be switched around. After making changes you will have to restart the Reminder service for these changes to be picked up.