We've talked before about ways to control a BitTorrent client from the iPhone, and some unofficial developers have gotten it working in a jailbroken way. But apparently that's as far as we'll get -- µMonitor, a little iPhone app to control µTorrent (a popular BitTorrent app that I use pretty often) was recently submitted to the App Store, and Torrentfreak reports that it's been rejected out of hand. This isn't the first time something like this has come up: Drivetrain, another torrent remote control tool, was also rejected back in May.
Apparently Apple tells the developer that they are disallowing all types of BitTorrent-related apps "because this category of applications is often used for the purpose of infringing third party rights." Often does not equal always, but technically that's another point: it's Apple's App Store, and they can take their ball and go home if they want. Torrentfreak claims that the myNZB app technically does the same thing (it basically controls a newsreader that can be used to download large numbers of files, possibly in violation of copyright), but it's the word "torrent" that Apple (and, likely, their content partners) have an issue with. Sure enough, a search of "torrent" on the App Store doesn't bring up anything related to the BitTorrent technology.
You can still run µTorrent on your iPhone, although you'll have to jailbreak it and dive into the Cydia repository, where it's listed under "Utilities." As for Apple's stance, I wouldn't hold your breath waiting for things to change on this one -- µTorrent isn't even an app that enables BitTorrent downloading; it just makes it easier (by accessing a client that's doing the work elsewhere), and if they aren't willing to pay heed to these distinctions now, it's not likely they'll bother in the future, either.