A lot of people want a close button for the Ubuntu notifications but unfortunately this won't happen - they don't want NotifyOSD to be customizable. But you can get notifications that have a close button by using the AWN Notifications Daemon.
CloudSN (Cloud Services Notifications) is an application similar to Specto (which is not maintained anymore): it can display notifications when you have new emails (POP3 and IMAP), new Identi.ca messages, Google Reader unread items or it can watch any RSS feed for changes.
Mumbles tries to bring a more Growl-like interface to Linux notifications. Currently it supports applications such as Firefox, Thunderbird, Amarok, and Twitter's API, among others.
This script notifies you when a contact comes online, goes offline, sends you a message, when they have a birthday soon or when a file transfer is completed.