//.NET Framework 2.0

Uri startupPath, targetPath;

startupPath = new Uri(Application.StartupPath + "\\");
targetPath = new Uri(value);

//startupPathから見た、targetPathを相対パスで取得する
Console.WriteLine(startupPath.MakeRelativeUri(targetPath).ToString());


//---------------------------------------------------------------

//.NET Framework 1.1

Uri startupPath, targetPath;

startupPath = new Uri(Application.StartupPath + "\\", true);
targetPath = new Uri(value, true);

//startupPathから見た、targetPathを相対パスで取得する
Console.WriteLine(startupPath.MakeRelative(targetPath));