I've just been playing around creating some eps files with gnuplot, and have subsequently had to convert them to PDFs for someone else to view. Turns out I wasn't aware of the following:
1) You can drag-and-drop pages within PDFs in Preview.app, to re-arrange the page order. You can also delete pages using the Edit menu (and add blank ones, if that floats your boat). More detail here.

Editing a PDF in Preview.app
I've also just discovered that you can use Cmd-R to rotate either a single page or all pages between portrait and landscape orientation.
2) If you're a fan of the command-line, there's a built-in script to join multiple PDFs. I originally found it on this blog (turns out they're investigating protein misfolding and aggregation, small world). Basically, you can find the script at the following location (all one line, obviously):
If you want to add the path to your .profile file, don't forget to put it in quotes otherwise OS X will baulk at the spaces. To use the script, just go like so…
I'm not suggesting these are particularly life-changing pieces of news, but I wasn't aware of them so thought I'd spread the love.