In a PC Magazine interview with Apple's Vice President of Hardware Product Marketing, Greg Joswiak, the executive said (though the is paraphrased and not quoted directly) that Apple is taking a neutral stance on native iPhone applications, and won't intentionally work to break their functionality or block their installation, though these breakages may be the unintended side effect of Apple software updates.
Sascha Segan, who spoke with Joswiak, writes:
"I asked him about independent, native software development for the iPhone. He said Apple doesn't oppose native application development, which was new to me. Rather, Apple takes a neutral stance - they're not going to stop anyone from writing apps, and they're not going to maliciously design software updates to break the native apps, but they're not going to care if their software updates accidentally break the native apps either. He very carefully left the door open to a further change in this policy, too, saying that Apple is always re-examining its perspective on these sorts of things."
For a full guide to installation of third-party applications for the iPhone, and which apps are actually useful, see our guide.