Manoj, I have tested on your site and email notifications are working.
Let me explain what I did in more detail.
I have loged in as userA >>went to "My Preferences">>and checked notifications to be sent "Immediately".
I loged off.
I loged in as userB>>and have sent userA a PM, friends request and have left a note on userA's newsfeed.
I checked userA's email and I have received the notification:
Note that email notifications will come only if:
1. User was loged out when notifications should have come. For example, userA should have been loged out from your site when userB have sent a PM to userA.
2. Email notifications are sent by CRON when any user refreshes any page on your site. 50 emails are sent every 10 minutes, giving that somebody refreshes the page within those 10 minutes.