I use the csc.exe compiler called from a .vbs script.
In your xyz.cs script, add the following lines after the directives (my example is for the Renci SSH):
using System;
using Renci;//FOR THE SSH
using System.Net;//FOR THE ADDRESS TRANSLATION
using System.Reflection;//FOR THE Assembly
//+ref>"C:\Program Files (x86)\Microsoft\ILMerge\Renci.SshNet.dll"
//+res>"C:\Program Files (x86)\Microsoft\ILMerge\Renci.SshNet.dll"
//+ico>"C:\Program Files (x86)\Microsoft CAPICOM 2.1.0.2 SDK\Samples\c_sharp\xmldsig\resources\Traffic.ico"
The ref, res and ico tags will be picked up by the .vbs script below to form the csc command.
Then add the assembly resolver caller in the Main:
public static void Main(string[] args)
{
    AppDomain.CurrentDomain.AssemblyResolve += new ResolveEventHandler(CurrentDomain_AssemblyResolve);
    .
...and add the resolver itself somewhere in the class:
    static Assembly CurrentDomain_AssemblyResolve(object sender, ResolveEventArgs args)
    {
        String resourceName = new AssemblyName(args.Name).Name + ".dll";
        using (var stream = Assembly.GetExecutingAssembly().GetManifestResourceStream(resourceName))
        {
            Byte[] assemblyData = new Byte[stream.Length];
            stream.Read(assemblyData, 0, assemblyData.Length);
            return Assembly.Load(assemblyData);
        }
    }
I name the vbs script to match the .cs filename (e.g. ssh.vbs looks for ssh.cs); this makes running the script numerous times a lot easier, but if you aren't an idiot like me then a generic script could pick up the target .cs file from a drag-and-drop:
    Dim name_,oShell,fso
    Set oShell = CreateObject("Shell.Application")
    Set fso = CreateObject("Scripting.fileSystemObject")
    'TAKE THE VBS SCRIPT NAME AS THE TARGET FILE NAME
    '################################################
    name_ = Split(wscript.ScriptName, ".")(0)
    'GET THE EXTERNAL DLL's AND ICON NAMES FROM THE .CS FILE
    '#######################################################
    Const OPEN_FILE_FOR_READING = 1
    Set objInputFile = fso.OpenTextFile(name_ & ".cs", 1)
    'READ EVERYTHING INTO AN ARRAY
    '#############################
    inputData = Split(objInputFile.ReadAll, vbNewline)
    For each strData In inputData
        if left(strData,7)="//+ref>" then 
            csc_references = csc_references & " /reference:" &         trim(replace(strData,"//+ref>","")) & " "
        end if
        if left(strData,7)="//+res>" then 
            csc_resources = csc_resources & " /resource:" & trim(replace(strData,"//+res>","")) & " "
        end if
        if left(strData,7)="//+ico>" then 
            csc_icon = " /win32icon:" & trim(replace(strData,"//+ico>","")) & " "
        end if
    Next
    objInputFile.Close
    'COMPILE THE FILE
    '################
    oShell.ShellExecute "c:\windows\microsoft.net\framework\v3.5\csc.exe", "/warn:1 /target:exe " & csc_references & csc_resources & csc_icon & " " & name_ & ".cs", "", "runas", 2
    WScript.Quit(0)