Probably your XP or Vista Recovery partition.
Have a look with Partition Wizard or a Linux live CD. Don't mess it up though. That's why it's protected.
As for the other missing stuff, HDDs never give their full nominal capacity.
And there are plenty of hidden files. eg Pagefile, hiberfil (for hibernation), restore points etc.
Google how to view hidden files if not turned on.
Download and Run Ccleaner to free up a bit of space if you want.
Consider a larger drive at some point. 40GB is a bit old and small these days.
250GB drives are quite cheap £20?