My experience
This is my first experience in VPS hosting. I was trying to install apache tomcat version 6 in my Godaddy VPS by using SSH. But is not worked. Then I found a very good article from the google. (http://www.mysamplecode.com/2012/05/java-tomcat-hosting-beginner-experience.html ) But It's not worked for me. Godaddy provided tomcat version 7 in their WHM cPanel. I installed it but tomcat 7 not supported in my webapp. It's getting 404 error in my webapp. Also I was trting to setup local server for tomcat 7 and it's getting me same error.
Then I try to solve this problem in 2 and a half day. I was googling and did what said in articles, ask from a friend who has some good knowledge in servers but they are unable to find a solution for it.. Finally I was call to the godaddy customer service for getting their help. But they said, they did not provided any installation support for 'Managed' VP servers.
Then I was realized, Ok, no one can help me in this case, But I have to do it, So how can I do this?
Then I destroy and rebuild the server and started form the beginning.
How to Install
Before you started, you need to enable root access. Godaddy provided a documentation for that.
If you want to install java please refer this documentation (Please do not install tomcat 7 version) - https://in.godaddy.com/help/how-to-install-apache-tomcat-12290
Then log in to your WHM cPanel and go 'Install an RPM' and install all the tomcat6 related component one by one.
After tomcat6 installation you can log into your VPS usinig putty (Hope to write putty configuration article in next time).
If you doing some changes in the server, you should have root permission. So switch to root user, type 'sudo su'. If you needs more help please refer this godaddy documentation ( https://in.godaddy.com/help/switching-to-the-root-user-on-your-linux-server-12330 )
Then go to your var/lib folder. You can see installed tomcat6 folder their. Then type 'sudo service tomcat6 status' to get your tomcat 6 status.
If status is stopped, You can run 'sudo service tomcat6 start' to start the server. Then tomcat6 will start in 8080 port. To check the Tomcat running enter the IP address of your VPS server and port 8080
http://yourVPSIPAddress:8080. 
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