If processing time is not the main concern, but if the main concern is file size (or a fine-grained control over certain features of the output file), then the Ghostscript way certainly offers more power to you. However, I agree with other answers: for your use case of merging PDF file types only, pdftk may be the best (and certainly fastest) option. You can even use it to merge a mix of PDFs, PostScript (PS) and EPS into one single output PDF file: gs \
You can also use Ghostscript to merge different PDFs.
