There are many answers to that question. Firstly in a PROD environment, I would notify the users before I deploy the app. If you need a high availability online system which should handle changes quickly, you could use a content management system (say vignette) to make content updates.
It may also depend on the server how this is done. Some are capable of detecting changes and automatically deploying the ear. You can also write an ant script to check out code, compile it, make an ear and then deploy it homogeneously to the PROD environment.
This question probably belongs in Job discussion. [ May 18, 2008: Message edited by: John Meyers ]