Q:

How to determine where biggest files/directories on my system are stored?

I was wondering how do you know where the largest files in my system are stored.
For example---
Disk Space Used: 1GB
Java: 500MB
Java Percentage: 50% maybe represented in a pie chart. Maybe?
I know this maybe a feature overkill. I sometimes forget having stored things and wonder why my disk is so full. 
So basically a command that will allow me to run on the file system and provide me with information on disk space used.
Please and thank you.

A:

The Disk Usage Analyzer is available under Ubuntu > Accessories > Disk Usage Analyzer. It provides you with a snazzy pie graph showing what files and folders take up the most space:

The documentation on it is a little sparse, but you can find more information on the Ubuntu wiki, and the project page.
If you're interested in using the command line, there's du which is described here.

A:

Unless it changed recently, baobab only shows directories; check out kdirstat for an alternative that actually shows files, coloured by type.
A commandline alternative is
du -a | sort -nr | head

A:

The solution that @UncleZeiv proposed is not working when there is really no more space left, since sort is using the /tmp folder when there are multiple lines to sort.
du -a | sort -nr | head
sort: write failed: /tmp/sortuCYq8E: No space left on device

An alternative is a combination of the answer from @UncleZeiv and @Yoav Weiss, plus adding another path for the temporary location:
sudo du -a | sort -nr -T /media/usb-key

Finally, my preferred solution will be a human-readable one that doesn't depend on temp folder and list root directory (/):
sudo du -ah --max-depth=1  / | sort -hr

