Compile C# code in standalone Unity http://answers.unity3d.com/questions/364580/scripting-works-in-editor-try-it-but-not-build.html

CSFactory.cs

  public void GenerateCSharpCode(CodeCompileUnit ccu, string filename)
    {
        // Generate the code with the custom C# code provider
        Modified.Mono.CSharp.CSharpCodeCompiler compiler = new Modified.Mono.CSharp.CSharpCodeCompiler();
        
        // Setup the compilation settings, write a DLL inside the Temp folder
        CompilerParameters compileOptions = new CompilerParameters();
        compileOptions.GenerateInMemory = false;
        compileOptions.GenerateExecutable = false;
        compileOptions.CompilerOptions = "/target:library";
        compileOptions.OutputAssembly = "Temp/" + Path.GetFileNameWithoutExtension(filename) + ".dll";
        
        // Add all the assembly references so the compilation can succeed (required if dependencies)
        foreach (var assembly in AppDomain.CurrentDomain.GetAssemblies()) {
            compileOptions.ReferencedAssemblies.Add(assembly.Location);
        }

        // Actually compile the code
        CompilerResults compilerResults = compiler.CompileAssemblyFromDom(compileOptions, ccu);

        // Print the eventual errors
        foreach (CompilerError compilerError in compilerResults.Errors)
            Debug.LogError(compilerError);

        // Load the compiled assembly in memory
        System.Reflection.Assembly.LoadFrom(compilerResults.CompiledAssembly.Location);
    }