You should just be able to format the partition in question, and re-install windows on that. If all your data is on other partitions, leave those alone and you're good.
As far as I can remember, Windows asks you which partitions you want to re-format during an install. The are also several live CDs with graphical tools that will let you edit and reformat partitions.
Are most of your programs also installed on
C:, or are they somewhere else? Once Windows is installed, all of the programs also have to be re-installed.
In the Windows default configuration, many programs will also have been saving their data to
C:, in your own personal
User folder. You might want to play safe and copy that out to another partition before you proceed.