If I want to merge some scans to one PDF file, I do this:
pdfjoin --a4paper --fitpaper false --rotateoversize false scan01.png scan02.png
This gives you a PDF document with DIN-A4 page size, where every png file is centered on it's own page. Images that are too big for one DIN-A4 page are resized proportionally to fit on one page. Smaller images are not resized (not made bigger).
You have to name all png files on the command line, but you can also use wildcards to eg merge all png files in the current directory:
pdfjoin --a4paper --fitpaper false --rotateoversize false *.png
The pdfjoin command is part of PDFjam as mentioned in the answer by Jeremiah Willcock. So you will most likely have to install a package named pdfjam or texlive-extra-utils with your distros package manager. PDFjam is able to use png files as input since Version 2.07, released in 2010-11-13.
