I’ve made a simple class to merge PDF files using iText#:

csharp:
using System;
 using System.Collections.Generic;
 using System.IO;
 using iTextSharp.text;
 using iTextSharp.text.pdf;

public class PdfMerge
 {
     private BaseFont baseFont;
     private bool enablePagination = false;
     private readonly List<PdfReader> documents;
     private int totalPages;

    public BaseFont BaseFont
     {
         get { return baseFont; }
         set { baseFont = value; }
     }

    public bool EnablePagination
     {
         get { return enablePagination; }
         set
         {
             enablePagination = value;
             if (value && baseFont == null)
                 baseFont = BaseFont.CreateFont(BaseFont.HELVETICA, BaseFont.CP1252, BaseFont.NOT_EMBEDDED);
         }
     }

    public List<PdfReader> Documents
     {
         get { return documents; }
     }

    public void AddDocument(string filename)
     {
         documents.Add(new PdfReader(filename));
     }
     public void AddDocument(Stream pdfStream)
     {
         documents.Add(new PdfReader(pdfStream));
     }
     public void AddDocument(byte[] pdfContents)
     {
         documents.Add(new PdfReader(pdfContents));
     }
     public void AddDocument(PdfReader pdfDocument)
     {
         documents.Add(pdfDocument);
     }

    public void Merge(string outputFilename)
     {
         Merge(new FileStream(outputFilename, FileMode.Create));
     }
     public void Merge(Stream outputStream)
     {
         if (outputStream == null || !outputStream.CanWrite)
             throw new Exception("OutputStream es nulo o no se puede escribir en éste.");

        Document newDocument = null;
         try
         {
             newDocument = new Document();
             PdfWriter pdfWriter = PdfWriter.GetInstance(newDocument, outputStream);

            newDocument.Open();
             PdfContentByte pdfContentByte = pdfWriter.DirectContent;

            if (EnablePagination)
                 documents.ForEach(delegate(PdfReader doc)
                                   {
                                       totalPages += doc.NumberOfPages;
                                   });

            int currentPage = 1;
             foreach (PdfReader pdfReader in documents)
             {
                 for (int page = 1; page <= pdfReader.NumberOfPages; page++)
                 {
                     newDocument.NewPage();
                     PdfImportedPage importedPage = pdfWriter.GetImportedPage(pdfReader, page);
                     pdfContentByte.AddTemplate(importedPage, 0, 0);

                    if (EnablePagination)
                     {
                         pdfContentByte.BeginText();
                         pdfContentByte.SetFontAndSize(baseFont, 9);
                         pdfContentByte.ShowTextAligned(PdfContentByte.ALIGN_CENTER,
                             string.Format("{0} de {1}", currentPage++, totalPages), 520, 5, 0);
                         pdfContentByte.EndText();
                     }
                 }
             }
         }
         finally
         {
             outputStream.Flush();
             if (newDocument != null)
                 newDocument.Close();
             outputStream.Close();
         }
     }

    public PdfMerge()
     {
         documents = new List<PdfReader>();
     }
 }

Usage:

csharp:
string basePath = "c:\\pdf";

PdfMerge demo = new PdfMerge();

demo.AddDocument(Path.Combine(basePath, "static-dynamic-typing-meijer.pdf"));
 demo.AddDocument(Path.Combine(basePath, "composable-memory-transactions.pdf"));

demo.Merge("mergedPapers.pdf");

Console.WriteLine("Archivo generado en: {0}", Path.GetFullPath("mergedPapers.pdf"));