Advantages/Disadvantages to exploded WAR files
I think that was my answer mentioning the exploded WAR in the other question. Exploded WARs are easier to navigate and you can deploy 'parts' of your application that much quicker (depending on how our Web/App server deals with this), e.g. Replace a single resource like a JSP page. However it can have some drawbacks:
Versioning - What version are you really running? "Hmmm, I'm not really sure now"
Security - Do you have the right permissioning in place for the exploded format?
Messiness - Files galore spread out all over your nice app/web server (some people really hate this).
Bottom line: I tend to go exploded for prototype Dev work and then move to proper packaging the closer to PRD I get.
The only real benefit you receive from deploying an exploded ear/war is the ability to hot-swap files on the server, as well as the time saved on the packaging (which IMHO is negligible).
Basically - this is a useful feature for development phases. I wouldn't choose this deployment method for a production environment.
There are also some web application servers which require exploded wars for some esoteric features, but this is nothing I've encountered in regular usage.
At the development stage is more confortable to deploy it exploded. This way you can hot update some deployed resources (as can be the JSP pages).
For Testing and Production environments, I prefer instead the packaged deployment: ligther, and easier to handle for the deployers.