What you want to use is:
Server.MapPath("/Content/filepath.ext");
This will give you the absolute path of a file based on it's position within the website, in this case, from the /Content directory.
For a program external to the website, you have a couple options;
The easiest to implement might be a simple configuration value in the external program which points to the directory. My guess is you've already decided that's not ideal, but it may be the quickest way.
Alternatively, there's a Microsoft .NET assembly which gives you easy access to IIS information (I can't recall its name off the top of my head!). You could use this assembly to find the appropriate website, and retrieve its root directory. I'll see if I can find it and get an example, or maybe someone else will see this and post an answer with that information.