Podcaster was the first high-profile application that got rejected. Podcaster allowed its users to download and stream podcasts directly, instead of having to download them through iTunes first, and according to Apple, this duplicated functionality of Apple's own iTunes. The author of the application defended himself by stating that it offers several features that Apple does not offer. In addition, loads of other applications in the App Store also duplicate functionality of default applications. Obviously, Apple is rejecting Podcaster because the company plans to add similar functionality in future iPhone/iTunes updates.
The case of MailWrangler is similarly odd, since the rejection email didn't make an awful lot of sense. MailWrangler allowed you to be logged in to multiple GMail accounts at the same time, and switch between them without having to log out, like you had to do when using mobile Safari. Apple rejected the application because it deemed it too similar to the included mobile Mail application, even though they are both rather dissimilar.
These rejections caused a tidal wave of criticism, because they appeared to be completely random. The applications didn't break any of the rules set forth by the iPhone's SDK agreement, so how are developers to know - beforehand - if their application is accepted or not? In an attempt to stop these criticisms, Apple has added an NDA clause to its rejection notices:
In other words, if you're an iPhone application developer, the process of designing and writing an application goes more or less like this. You spend quite some time thinking of an idea, and then you set out to design your application. After weeks and months of painstakingly implementing your idea as a working iPhone application, you submit it to the App Store, and cross your fingers hoping all your work hasn't been in vain. Sadly, it appears that you broke some invisible rule, or you duplicated default functionality even though you didn't, or you inadvertently came up with an idea Apple was already working on for a future iPhone revision - and your application is rejected. And you're not allowed to talk about it. Your wife (or husband) is really going to wonder what you've been doing all those weeks in your basement.
These policies from Cupertino are devastating for developer confidence, and one high-profile developer (of Exposure) has already stopped developing applications for the current App Store. I'm out, he says. "'I'm out' doesn't mean I'm pulling Exposure from the store. All it means is I'm not going to invest time and money into new ideas for the iPhone until this mess is resolved."