
Para poder utilizar este código deben bajarse la librería iTextSharp (http://sourceforge.net/projects/itextsharp), y referenciar esta DLL y «System.Security» desde su proyecto.
A continuación les dejo el código:
using System;
using System.Collections;
using System.IO;
using System.Security.Cryptography;
using System.Security.Cryptography.Pkcs;
using iTextSharp.text;
using iTextSharp.text.pdf;
using Org.BouncyCastle.X509;
using SysX509 = System.Security.Cryptography.X509Certificates;
/// <summary>
/// Helper para el firmado de PDFs con la librería iTextSharp
/// </summary>
public static class PDF
{
    /// <summary>
    /// Firma un documento
    /// </summary>
    /// <param name="Source">Documento origen</param>
    /// <param name="Target">Documento destino</param>
    /// <param name="Certificate">Certificado a utilizar</param>
    /// <param name="Reason">Razón de la firma</param>
    /// <param name="Location">Ubicación</param>
    /// <param name="AddVisibleSign">Establece si hay que agregar la firma visible al documento</param>
    public static void SignHashed(string Source, string Target, SysX509.X509Certificate2 Certificate, string Reason, string Location, bool AddVisibleSign)
    {
        X509CertificateParser objCP = new X509CertificateParser();
        X509Certificate[] objChain = new X509Certificate[] { objCP.ReadCertificate(Certificate.RawData) };
        PdfReader objReader = new PdfReader(Source);
        PdfStamper objStamper = PdfStamper.CreateSignature(objReader, new FileStream(Target, FileMode.Create), '\0');
        PdfSignatureAppearance objSA = objStamper.SignatureAppearance;
        if (AddVisibleSign)
            objSA.SetVisibleSignature(new Rectangle(100, 100, 300, 200), 1, null);
        objSA.SignDate = DateTime.Now;
        objSA.SetCrypto(null, objChain, null, null);
        objSA.Reason = Reason;
        objSA.Location = Location;
        objSA.Acro6Layers = true;
        objSA.Render = PdfSignatureAppearance.SignatureRender.NameAndDescription;
        PdfSignature objSignature = new PdfSignature(PdfName.ADOBE_PPKMS, PdfName.ADBE_PKCS7_SHA1);
        objSignature.Date = new PdfDate(objSA.SignDate);
        objSignature.Name = PdfPKCS7.GetSubjectFields(objChain[0]).GetField("CN");
        if (objSA.Reason != null)
            objSignature.Reason = objSA.Reason;
        if (objSA.Location != null)
            objSignature.Location = objSA.Location;
        objSA.CryptoDictionary = objSignature;
        int intCSize = 4000;
        Hashtable objTable = new Hashtable();
        objTable[PdfName.CONTENTS] = intCSize * 2 + 2;
        objSA.PreClose(objTable);
        HashAlgorithm objSHA1 = new SHA1CryptoServiceProvider();
        Stream objStream = objSA.RangeStream;
        int intRead = 0;
        byte[] bytBuffer = new byte[8192];
        while ((intRead = objStream.Read(bytBuffer, 0, 8192)) > 0)
            objSHA1.TransformBlock(bytBuffer, 0, intRead, bytBuffer, 0);
        objSHA1.TransformFinalBlock(bytBuffer, 0, 0);
        byte[] bytPK = SignMsg(objSHA1.Hash, Certificate, false);
        byte[] bytOut = new byte[intCSize];
        PdfDictionary objDict = new PdfDictionary();
        Array.Copy(bytPK, 0, bytOut, 0, bytPK.Length);
        objDict.Put(PdfName.CONTENTS, new PdfString(bytOut).SetHexWriting(true));
        objSA.Close(objDict);
    }
    /// <summary>
    /// Crea la firma CMS/PKCS #7
    /// </summary>
    private static byte[] SignMsg(byte[] Message, SysX509.X509Certificate2 SignerCertificate, bool Detached)
    {
        //Creamos el contenedor
        ContentInfo contentInfo = new ContentInfo(Message);
        //Instanciamos el objeto SignedCms con el contenedor
        SignedCms objSignedCms = new SignedCms(contentInfo, Detached);
        //Creamos el "firmante"
        CmsSigner objCmsSigner = new CmsSigner(SignerCertificate);
        // Include the following line if the top certificate in the
        // smartcard is not in the trusted list.
        objCmsSigner.IncludeOption = SysX509.X509IncludeOption.EndCertOnly;
        //  Sign the CMS/PKCS #7 message. The second argument is
        //  needed to ask for the pin.
        objSignedCms.ComputeSignature(objCmsSigner, false);
        //Encodeamos el mensaje CMS/PKCS #7
        return objSignedCms.Encode();
    }
}
Espero que este código les sea de utilidad.
Suerte!

