Naming conventions in the java world....

We are making the move from all green-screen RPG to browser based apps. We are 
going to start with RPG CGI, and JSPs and move towards true java applications. 
I think we have a good handle on how to name and organize the traditional 
library based objects (RPG, PFs, CLP, etc) but we are not sure on how best to 
organize the IFS directory based objects. I would be interested in hearing any 
do/don't recommnedations from people who are already there. We are not sure if 
we should just have one directory in the IFS with all of our IFS based objects 
(with appropriate subdirectories by object type (HTML, Images, JSP, Java), or 
if we should organize by System (Student Records, Admissions, Financial Aid), 
or if we should organize by Application (Class Scheduling, Class Rosters, etc). 
When we eventually get to deploying applications via EAR or WAR files will the 
organization we choose be a factor.