It takes space of your desktop and can be quite irritating as well. With the help of the Ubuntu's Unity indicator support, someone has written a libappindicator compatible plug-in which for Evolution which notifies whenever you receive new mails without distracting. The indicator is called Evolution Indicator.
If you use Ubuntu 11.04 Natty Narwhal, then you can install Evolution Indicator by using the below command.
sudo add-apt-repository ppa:goehle/goehle-ppa
sudo apt-get update
sudo apt-get install evolution-indicator