It seems that the days when you needed to keep you computer clean and tidy are gone. With the operatingsystems only require a few percent of your harddrive this might be less of a problem. But my experience is that it still fills up and you may lose focus from the “system-near” files and
only try to clean up your other data (like larger mediafiles or old backups).
I most recently used this tool when my Windows-partition on my work-laptop.
jDiskReport – Cross platform using java (Mac/Windows/Linux)
There are many similar tools for both Windows and Linux. jDiskReport is the best free one I’ve found.
In Ubuntu you can install a gnome tool but I don’t remember the name of the package right now. I will update this when I do. For KDE there is Filelight. But I haven’t tried it yet.
This Google-page has a summary of a bunch.