Thank you all for your requests and suggestions. I have implemented some of them in this version. I will keep adding new features in it.
You can download Sohail's Gmail Notifier for Google Apps which runs on Windows 7 from the following link.
http://gmailnotifier.net/files/folders/sohailsgmailnotifierforgoogleappsmultipleaccountsv11/entry367.aspx
Please let me know if you find any issues with the notification window. You would need to run this notifier as an admin.
Thanks