So, which is the best utility? Just for its sheer number of features, you should consider pdfmeld. I've used Ghostscript for years and still have a soft spot for it. But typing those long strings of options really wears me out. As for joinPDF, it's a great too for getting the job done quickly.
If you're a Linux user who only uses free and Open Source software, then choose Ghostscript or joinPDF. But if you don't mind paying for software, pdfmeld is a great little application which handles all of your PDF merging needs.