If I am upgrading from 11.10 to 12.04 , then will my applications be deleted and also will my already configured mail setting deleted? I have many mails in my Inbox.
For your applications when upgrading you have a arrow next to the to be deleted text.
As with all OS upgrades there is an important rule to follow:
Having said that, there is only a small risk that you lose data during an upgrade process. All your private data, e-mails, and application settings will be kept. Only those applications you installed other than from the Ubuntu repositories may have to be reinstalled later, but settings for these applications will be kept too.
This is especially true for applications you installed from a ppa, from a dowloaded .deb package or compiled yourself.