I was reading this Ubuntu Software Center design document and wondering, what software was used to design all those ui concept?
Those specific designs are made by hand by Matthew Paul Thomas on graph paper.
I've found Pencil to be most valuable when I need to pump out quick little UI mocks. It's a Firefox extension by default but you can also get a version that runs on XUL (the framework beneathe Firefox).
While it might not be what was used for this example, it's worth a look.
Balsamiq Mockups is an application that occasionally gets used by Mark and the design team.
It's not free but it is cross-platform (through Java) and provides a lot more features than Pencil.
WireframeSketcher lets you do this kind of mockup. You can use it as a standalone tool but also as a plugin for Eclipse-based IDEs (like Aptana and Zend Studio).