In ONET.XML, you can add  a reference to a JavaScript file. But modifying ONET.XML isn't recommended by Microsoft.

Guidelines to Centralize SharePoint Style/Script Customizations:
mindsharpblogs.com/.../1006.aspx

is there a way to add  script without using the CEWP? AllItems.aspx, for example, cannot host web  parts.

Yes, my post describes how to add  script from an instance page, to a direct-mode
page, to all pages  in a site  definition, to all pages in the entire farm.

However, the AllItems.aspx page IS a web  Part page and CAN host web parts. This
was an untested scenario when Microsoft released WSS v2 so it isn't supported in
the UI. Check out this post for how to add script to an instance of the
AllItems.aspx page:
mindsharpblogs.com/.../285.aspx

Of course, there are also direct-mode pages on the file system in the 60 hive
that provide the template for the ghosted version of the list page. They can be
found in the site definition where the list is defined.