I stumbled across this on Amazon last week.  It's a two-port Atari 2600 (and related) controller to USB adapter:
http://www.amazon.com/Atari-PC-USB-Cable-RETROLINK-2600/dp/B007ZS35CU/ref=sr_1_11?s=videogames&ie=UTF8&qid=1341873193&sr=1-11
Not sure how long this product has been around.  There are several vendors on eBay and Amazon offering it.  I couldn't find a website for the manufacturer (Retrolink).  But it was cheap ($8 + shipping, or just under $13 shipped from the Amazon vendor), so I took a gamble.
Initial results were not encouraging.  The Asrock board in my cabinet didn't recognize the adapter, either in XP (showed up as a USB device requiring a driver) or in OS X.  No drivers or documentation were included (not even the box seen in the photo), and no website could be found.  I was about to toss it, then figured I might as well try it on a different computer.  Plugged it into my main machine (Gigabyte i7 board), and it popped right up.  Worked in Stella with no configuration at all.  So I scrounged up an old USB PCI card, installed that in the cab, and bang:  Atari goodness.
The Retrolink adapter (assuming your motherboard recognizes it) works out of the box with Stella, no configuration required.  My 30-year-old Atari joystick plays perfectly.  Ditto for the (also) 30-year-old Colecovision controller, although that emulator does have to be configured in Preferences (Mugrat) before playing.  I still need to dig out a set of Atari paddles and see how it works with those.
So: Assuming it works with your mobo, we have a new champ as far as cheap hookups for Atari 9-pin controllers.  At $13 shipped, it's just over a third of the cost of a Stelladaptor, and about $10 (shipped) cheaper a single Legacy Engineer USB knockoff stick.   
