iAlert: Notification for Apple Mail, iTunes, etc
iAlert is a system preference pane that enables notification for a range of apps, including iTunes, Safari, Firefox, Thunderbird, Entourage and most importantly, Apple Mail.
It runs on top of SIMBL (Smart InputManager Bundle Loader), the same Cocoa application hack that powers the Safari plug-in PithHelmet. A copy of SIMBL in included in iAlert’s disk image and must be installed first.
When enabled, iAlert displays very pretty smoked-glass alerts. The iTunes ones are nice. The Mail.app one looks like this (the example shows some of the variables it can display):

If you click on the alert, a range of options pop up allowing you to interact with the message:

From left to right, they close the alert, open the iAlert preference pane, toggle the “do not disturb” mode, bring the app that launched the alert to the front, open the message in Apple Mail’s preview pane, reply, reply all or forward the message, mark the message as read or junk or move it to the trash.
The alerts can be customized by adding or removing a number of variables for each app’s iAlert scripts.
It is free (donations accepted) and can be downloaded from the developer’s website.
UPDATE: An improved version was released on 21 November 2005.
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October 30th, 2005 at 8:00 am
[...] So many notification options exists for Apple Mail — “loud” ones like iAlert or MailAppetizer, discreet ones like MailUnreadStatusBar, spoken ones like the Announce Mail or Spoken Sender Applescripts — that it is possible to overlook Mail’s built-in notification features. [...]
November 21st, 2005 at 8:41 am
[...] iAlert, the notification utility that runs on top of SIMBL, has been updated. [...]
December 28th, 2005 at 8:52 am
[...] It requires SIMBL, (Smart InputManager Bundle Loader), the same Cocoa application hack that powers the Safari plug-in PithHelmet and iAlert, a Mail.app (and more) notification system. [...]