For those of you who do not feel like going through the entire alerttemplates.xml file I recently had to do it for a client who wanted larger fonts in the emails that were sent out for alerts and notifications. I changed all fonts to Tahoma 12pt except for the Header which was already large enough. Nothing fancy. Just throwing it out there.
NOTE: Never modify the alertstemplates.xml directly. Make a working copy and use it with the stsadm command.
Drop the file onto your server and run the following stsadm command:
Syntax: stsadm -o updatealerttemplates -url {sitecollectionurl} -f {CustomAlertTemplate XML File}
Example: stsadm -o updatealerttemplates -url {sitecollectionurl} -f C:\customalerttemplates.xml
Remember, this is per site collection and you have to re-run the command each time you update the template as it stores the alert format in the database.
MSDN Description of Pre-defined Alert Templates: http://msdn.microsoft.com/en-us/library/bb802738.aspx
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