I wrote a blog entry on my company’s Blog with some tips on deployment of Application Express applications. It describes the pitfalls on manual and automatic deployment, and other useful tips.
You can find it here on the Whitehorses blog.
Excerpt
The most common method of deployment in Apex is to export the application via the web interface, and import it into another. However, there are some things you need to consider, such as supporting objects and shared components. Also, administrators have their own requirements, such as that all deployments should be scriptable. This can lead to problems.
If you have any comments or questions, feel free to place a comment here or on the Whitehorses site and I’ll update the blog.