Ashutosh, It appears like staging is the biggest problem. I'd start with that table first and get things cleaned up. Not only should you look in the Staging app but query the database table
staging_task directly to get a record count as there could be orphaned tasks in there from adding/removing servers while tasks were being logged.
The second thing I'd look at would be analytics. Make sure they are being cleaned up so you don't have GB of data being stored in there. If you're not using it at all, stick with Google Analytics and simply clean the data up and turn it off in Kentico.