To customize contents of built-in alerts, you can modify
alerttemplates.xml file under a folder \Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\1033\XML.
That file defines a format of alert emails and Query by CAML for each list.
For example, if you want to modify an alert content for a document library, open the file, find a line <AlertTemplate Type="List" Name="SPListTemplateType.DocumentLibrary">
and make required modifications to HTML contents surrounded by <AlertTemplate></AlertTemplate> tags as you like.
Once it's saved, do IISRESET, and you will an alert as you modified.
You may change a location or a file name of the lerttemplates.xml by stsadm command. If you decide to place your file to C:\template, you can do it as below.
stsadm -o updatealerttemplates -url http://<YourServer
-filename c:\template\<XML File> -lcid 1033
Note this rider (but I suspect the above info will still be correct ...)
Please note that XML structure and definition are not finalized yet so that they could still be changed between now and RTM release. Also regarding detailed usage of CAML within the file, please wait for SDK updated in a later release.