You can also use Ghostscript to merge different PDFs. You can even use it to merge a mix of PDFs, PostScript (PS) and EPS into one single output PDF file:
gs \
-o merged.pdf \
-sDEVICE=pdfwrite \
-dPDFSETTINGS=/prepress \
input_1.pdf \
input_2.pdf \
input_3.eps \
input_4.ps \
input_5.pdf
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.
Update:
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. To highlight a few of the differences: