The location of the repository depends a bit on which version you're talking about. Version 4 uses a relational database (Oracle, DB2 etc) to store the repository, while version 5 uses a directory strutcure stuffed with xml-files. I personaly prefer the xml-files, but maybe that's just me
As to what's actually stored in the reposity: it all the settings for your different application servers (where to log stuff, what heap size to use, which user to run under etc). The admin repository also contains things such as which applications you have installed, under which appserver they execute and so on. I also think that the bindings for EJB:s are stored in here (but I'm not sure about this, they could be in the installedApps folder, someone else might clarify this)
Additionaly, the repo contains the configuration for all your resources (jdbc connection pools, MQ queues, J2C connector etc).
References and documentation for WAS can be found in the WebSphere info center
or at IBM redbooks
hope this helps