There's been some confusion on this topic due to the reporting of the iPhone SDK event, but it appears that the $99 fee required to publish your applications to the iTunes App Store is an annual charge.
From Apple's press release:
The Standard Program costs $99 (US) per year and gives members an iPhone SDK and development tools; access to pre-release iPhone software; technical support; the ability to get code onto iPhones for testing; and distribution of applications via the new App Store.
To sum up:
- iTunes App Store to browse, purchase and download iPhone apps
- Developers set the price and get 70% of revenue. Apple keeps 30% for their costs.
- Applications must be approved by Apple and apps are available exclusively through the App Store
- No charge to distribute free applications, but you still have to pay the $99/year fee.