PDF Combine Pro can combine files within folders. For example, you have 3 folders with different file types inside each. The app can produce three combined PDF files.

It can easily create bookmarks that can be used as table of contents.
Users can add custom Cover pages to the combined PDF.
Legal users will appreciate the flexible bates stamping option.
Transparent user interface and full command line support.

Features :
Combines PDF, DOC, HTML, XLS, TIFF, PNG, JPEG files into PDF
Creates table of contents
Adds Back to Content link to the footer of each page
Inserts a Cover page of your choice
Combines PDF files by folders
Combine PDFs by common name part
Creates bookmarks out of file names or titles
No need for Adobe Acrobat
Command line
Clean graphic user interface
ActiveX and Server version

Whats new:
Updates: official site does not provide any info about changes in this version.

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