Instead of the regular pop-up, it would be really nice to be able to use the built-in Gnome "notify-send" command to get unobtrusive notifications using this built-in notifier. Implementation should be fairly straightforward, I think.
I could presumably do this manually via the "When new mail" command, but I don't know how to get gnubiff to pass the mail information (date, sender, subject) into the custom command... is there a custom string token, e.g. %s, that gnubiff will replace with this information? If so, what is the token? (There is no documentation on this.) If not, it would be nice to just get this feature built in (so we can select it with a checkbox, just like the regular pop-up, which I don't use because it's more obtrusive).
Similar functionality is available in MacBiff (using Growl, the Mac equivalent of libnotify), so you might be able to modify their code for this purpose (MacBiff is GPL'd).