Need to merge multiple pdf's into a single PDF with Table Of Contents sections

And what's the best tool for us to merge the pdf's?

On Linux (as well as on Windows), you can install an useful little program, pdftk. It works well to bind PDF's together. For example:

$ pdftk in1.pdf in2.pdf in3.pdf in4.pdf in5.pdf in6.pdf cat output out.pdf

where in*.pdf are the input files and out.pdf is the result. In between, @jerik already gave an answer how to deal with the TOC.

With Version 1.45 - December 6, 2012 is pdftk able to create bookmarks with update_info, which could be used as toc.

Its done in 3 Steps:

Precondition for my example

3 PDF files. Single page.

page1.pdf
page2.pdf
page3.pdf

1. Create the bookmark information

# build the bookmark out of an example file
pdftk page1.pdf dump_data output meta.txt
# Edit meta.txt as you need

Heres an example that worked for me, meta.txt:

InfoBegin
InfoKey: Creator
InfoValue: PDFTK
NumberOfPages: 3
PageMediaBegin
PageMediaNumber: 1
PageMediaRotation: 0
PageMediaRect: 0 0 595.32 841.92
PageMediaDimensions: 595.32 841.92
BookmarkBegin
BookmarkTitle: Page 1
BookmarkLevel: 1
BookmarkPageNumber: 1
BookmarkBegin
BookmarkTitle: Page 2
BookmarkLevel: 1
BookmarkPageNumber: 2
BookmarkBegin
BookmarkTitle: Page 3
BookmarkLevel: 1
BookmarkPageNumber: 3

2. Create an temporary merged pdf file

pdftk page* cat output temp.pdf

3. Add the bookmarks to the pdf

pdftk temp.pdf update_info meta.txt output final.pdf

When you open the final.pdf in acrobat reader you see the bookmarks on the left side.