I am having a custom singlestack built that will be set up in both .40 and 9mm. I've read up on the mags a good bit, and from what I have read, I am going to start with some from these two companies and see which I like best:
has several options in their "Cobra Mag". A flush fitting 9 rounder, a 10 rounder that sticks out just a bit, and an unlisted "system mag" that I ordered two of that hold 10 and barely stick out of the bottom of the gun. This mag will fit in the USPSA box. In singlestack division, I would have to download to 8, but I could use the same mag for L10 or to shoot steel or just plink with. If you are interested, call them and tell them you are interested in the "system mag". They will ask if you plan on shooting mostly factory or loading long. If the latter, you will want the 10mm mags. Virgil Tripp knows how to make a singlestack .40 run, and they are willing to answer questions and help out.
Wilson Combat also makes 9 rounders, either 47FX or 47NX (former is .40, latter is 10mm). They are supposed to be very good magazines. I also understand that Wilson Combat .45 ACP 8 round magazines (47D I think?) work just fine in a .40, so if you are or a friend have some lying around, give them a try.
Hope that helps.