How to create a TOC when merging documents?

Document document = new Document();
PdfCopy copy = new PdfCopy(document, outputStream);
PdfCopy.PageStamp stamp;
document.open();
PdfReader reader;
ListInputStream> pdfs = streamOfPDFFiles;
ListPdfReader> readers = new ArrayListPdfReader>();
IteratorInputStream> iteratorPDFs = pdfs.iterator();
for (; iteratorPDFs.hasNext(); pdfCounter++) {
    InputStream pdf = iteratorPDFs.next();
    reader = new PdfReader(pdf);
    readers.add(reader);
    pdf.close();
}
int currentPageNumber = 0;
IteratorPdfReader> readerIterator = readers.iterator();
PdfImportedPage page;
int count = 1;
while (readerIterator.hasNext()) {
    reader = readerIterator.next();
    count++;
    int number_of_pages = reader.getNumberOfPages();
    for (int pageNum = 0; pageNum  number_of_pages;) {
        currentPageNumber++;
        page = copy.getImportedPage(reader, ++pageNum);
        ColumnText.showTextAligned(stamp.getUnderContent(),
            Element.ALIGN_RIGHT, new Phrase(
                String.format("%d", currentPageNumber),
                new Font(FontFamily.TIMES_ROMAN,3)), 50, 50, 0);
        stamp.alterContents();
        copy.addPage(page);
    }
}
document.close();

You're asking for something that should be trivial, but that isn't. Please take a look at the MergeWithToc example. You'll see that your code to merge PDFs is correct, but in my example, I added one extra feature:

Text text = new Text(String.format("Page %d", pageNo));
entry.getValue().copyPagesTo(i, i, pdfDoc);
if (i == 1) {
    text.setDestination("p" + pageNo);
}
doc.add(new Paragraph(text).setFixedPosition(pageNo, 549, 810, 40));

For every first page, I define a named destination as a local destination. We use p followed by the page number as its name.

We'll use these named destinations in an extra page that will serve as a TOC:

PdfDocument tocDoc = new PdfDocument(new PdfReader(src3));
tocDoc.copyPagesTo(1, 1, pdfDoc);
tocDoc.close();
float y = 770;
for (Map.Entry entry : toc.entrySet()) {
    Paragraph p = new Paragraph();
    p.addTabStops(new TabStop(500, TabAlignment.LEFT, new DashedLine()));
    p.add(entry.getValue());
    p.add(new Tab());
    p.add(String.valueOf(entry.getKey()));
    p.setAction(PdfAction.createGoTo("p" + entry.getKey()));
    doc.add(p.setFixedPosition(pdfDoc.getNumberOfPages(), 36, y, 595 - 72));
    y -= 20;
}
for (PdfDocument srcDoc : filesToMerge.values()) {
    srcDoc.close();
}

In my example, I assume that the TOC fits on a single page. You'll have to keep track of the y value and create a new page if its value is lower than the bottom margin.

If you want the TOC to be the first page, you need to reorder the pages in a second go. This is shown in the MergeWithToc2 example.

Click How to create a TOC when merging documents? if you want to see how to answer this question in iText 5.