And here is one of those reasons:
When you created a new sitecollection using SPS2003, you were prompted with a screen that required you to fill in an owner of that particular sitecollection. If users were added to the site, the 'From' field of the email was the one of the sitecollection owner. So if users were confronted with access problems they could immediately email the site collection owner to fix those problems.
Now in 2007 you only have the 'To' field and the 'From' field is being used from the webapplication settings and therefore is a global email address. So users cannot 'simply' reply to the sent email.
Does someone know how to setup a different 'From' emailaddress for each sitecollection?