Handy Commands to troubleshoot linux box

Some handy links for troubleshooting linux machine.

http://www.cyberciti.biz/faq/show-all-running-processes-in-linux/.

Another link contains a video on top command (helpful) : http://www.linuxnix.com/2011/08/linux-top-command-explained-2.html

I am trying to solve a problem on my linux box, the error is very similar to this : http://serverfault.com/questions/301531/java-eats-100-cpu-up, but it keeps me baffled.