The analyses suggested so far have been static and high-level. What follows are a few lower-level analysis areas that may apply to your system. Each of these short sections could justify their own chapters (or even whole books) but I will just give a few pointers for brevity.
If I've missed out anything you consider important, please email and let me know – perhaps you're working on a type of system I've not come across before.
Database Schemas
There will be a data model (object/class model or data structure) within the application code and probably a separate one within a database. It is very common for these to be out of sync or for one to be a subset of the other. The database in question may be a traditional SQL one or something more unusual – currently, NoSQL databases are becoming popular but there is nothing new about changing trends and fashions in databases.
Fortunately, most databases follow a standard (SQL especially...