Gold acknowledged Apple's argument that it should be allowed a certain level of control over software for security purposes. But he noted Apple's occasional banning of other programs simply because they compete with Apple's own software -- one case being the Opera Web browser.
"That's not the way efficient markets work," Gold said. "It's not right and it really does stifle innovation."
iPhone developer Tony Bove said he wouldn't use a jailbroken iPhone for ethical reasons, but said Apple might actually might benefit from Cydia and others.
"A lot of time innovation pops out of these efforts," he said. "At the very least, Apple might learn something about its security."
But he thinks users are taking a risk that might not be worth it. "You take an application like video recording. Apple is definitely going to make use of the iPhone's camera for video conferencing and these other apps probably won't even work when Apple decides to release their own."
But so far, Freeman's efforts are paying off. He said he can barely keep up with developer and consumer interest as he looks to outsource some of the support and possibly add staff to his one-person operation.
He's also running Cydia while continuing his studies as graduate student at the University of California at Berkeley, Santa Barbara.
Freeman admitted that the Apple App Store is easier to use than his rival. But he's in the process of simplifying Cydia with changes he expects to go live later tonight. Currently, a user has to first go to an application's individual software provider to pay a program featured on Cydia, but Freeman said he's about to enable an Amazon-powered payment system that will bring Cydia more in line with the simplicity of the App Store.
Still, Freeman said Apple could cut off at least half his business if it just "wasn't so stubborn."
One example stems from his earlier, thwarted efforts to gain traction with Winterboard, a free program he wrote that lets iPhone users change any graphics or wallpaper on the device.
Freeman said it's become the most popular application he's offered through Cydia because iPhone users want to be able to customize the look of the device with sports themes and other graphics. It also sparks interest in other Cydia apps.
"If Apple allowed people to have their own wallpaper and allowed video recording apps, it would cut 50 percent into my market," he said. "But people see those things at Cydia and they stay and look for more."
This article was first published on InternetNews.com.