Well as you can imagine there are pros and cons to each one. So I should list a few so you can see where you might to go with this...
Databases
Pros
1) They tend to be more structured
2) They have referential integrity to help protect against corruption of data
3) If done correctly they can help format the type of data you are getting (won't allow you to enter a string in an integer field).
Cons
1) You have to connect and use a database. Which in itself can bring problems if you don't have one or not versed in SQL.
2) Little more time to setup and make available.
3) If the database goes down, you could have a lot of people's copy of the software not working.
Files
Pros
1) They are easy to setup and populate.
2) They allow the user to look at them and edit if need be.
3) Typically they are easy to load because they are local.
Cons
1) If the user can look at them and edit, they can also screw up the file.
2) When they get big in size they can be bulky, especially if you need to search.
3) There is no integrity checking to make sure that what is written to the file is in the format it should be in.
Personally if you are going to have a lot of parameters or a variable number of parameters that could end up being a lot, a database would be the way to go. They are structured, can be easily indexed and searched, and often times server-side languages can query and drop the content straight into an object (mysql_fetch_object() for instance in PHP). I would think you would make your reports using a custom report object so that you can easily manipulate reports and juggle them around, sort them etc. But that is just a design idea.
It is up to you to find which fits better with your scheme and how you, and your users, might use the software.
Hope that helps
This post has been edited by Martyr2: 14 Dec, 2007 - 09:54 AM