Firstly, I'm a software developer and not qualified as any kind of system or server expert so I'm looking for advice in order to help me prevent faults on our server.

I've written a modular system to carry out certain tasks for us autonomously to prevent us from writing the same old code over and over again. This consists of a Windows Service (.NET), a Web Service (WCF), a shared Class Library, and a Database which will run on a Windows Server 2003.

The problem comes, for me, in deployment. Specifically the web service - naturally the local service (and required shared library) are persisted (by default and convention) in the Program Files folder, but storing the web service here just seems absurd to me (even though we'd lock it down to appropriate use only).

Should the files be stored some place else all together? Or split them up and store the web service elsewhere?