Here's a quick shell command to work out where your disk space is being used. 
du -s * | sort -n | tail
If you run this in a directory it will print out the top files and directories under the current directory using up space. For example, yesterday I started playing with a Fuzzing tool for testing shopping cart. Unfortunately Xdebug was setup to save execution traces and profiling files on the server. The end result after about an hour of fuzzing was a directory with about 67 Gigs worth of files in it. That command let me track down the cause of the hard drive filling up quickly.