While not specifically about deploying PHP applications, Ian Barber's talk at the recent ThinkVitamin Code Management and Deployment Conference is packed full of good tips you can use in your web application deployment. He talks about everything from version control strategies, continuous integration, remote releases, package management, hotfixes and one of the most difficult things to do - rollback.
Still deploying sites and updates manually via FTP? This session will cover a number of automated deployment methods, best practice workflow for updating sites and fixing bugs, along with how to use staging servers, deploying to multiple machines, zips tars & scripts, packaged releases hotfixes, database changes, rollbacks and more.
There's tons of technologies mentioned, so you'd be better off going through his slides and taking your own notes. Unfortunately, a recording of the session isn't currently publicly available, but the slides are an excellent resource for those currently looking to better their overall deployment process.