As David points out, most apps that store data files don't support folders. But, some apps, like Goodreader, do.
But here's another approach - Use one of the "file" apps that read and write files with the computer, Dropbox and/or iDisk. These will support their own folders. Then, when you want to view or otherwise access a file in another app, like Pages, you just open the file app, go to the right folder, tap the filename and choose "open in". The file apps can be thought of as a file manager. For file management, you can do it one of two ways: 1) leave your file(s) on the source and access when needed, 2) sync file(s) from source into the file app and place in a specific folder.
The reason for using such a file app and keeping files in a central location is that the iPad does not have a file system like a computer. Each app keeps its own files within its "sandbox". So if you want a PDF file viewed using two or three apps, you have to keep two or three copies of the PDF file, one in each app. Of course you can delete the file in any app once you are done. The point is, you can't have an assortment of apps accessing the same file directly.
Some such apps are: Cloud Connect (my current favorite), and iFiles.
