You could write an external program, then use PHP's exec (or was it system?) function to interact with the executable or script.
Seems like the most sane way to do it. Another good alternative is to build a program or script that controls an external device that can communicate with a RESTfull type API exposed via HTTP - and then use lib_curl in PHP land to talk back and forth between it. Believe me, building a basic HTTP server in C++ that can be used to be remote controlled with PHP (or JS for that matter) is very simple.
Wait
I think I read the question wrong ;)
If you want to get into really cool stuff, I say that you learn C++. C++ is a great language that not only opens a lot of doors, but also provides a good learning experience. C++ is lots and lots of fun.
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In the case with USB its a bit different and more complicated (as USB has an established protocol and such) but serial is as easy as dumping data into a handle.
You should be able to pick up C++ to get to that point fairly soon. Either way it's a great experience.