You can't create folders for file storage on the iPad like you can on a computer. On the iPad, documents are stored in an app that is compatible with that particular file type. An app that can save, edit or create that file type is what you need.
For PDF files, there are free apps such as Apple's iBooks and Adobe Reader. Both apps will store PDFs for viewing,, but Reader will lay to annotate the PDFs. There are scads of other apps that work with PDFs, but these two are free.
For the MS office files, Word, Excel and PowerPoint compatibility there apps available in the app store like Quick Office Pro and Documents to Go. Take a look at those and see what you think. Apple also has their iWorks suite of apps, Pages, Numbers and Keynote that are compatible with the MS Office apps.
You can email files to the iPad, use something like DropBox to transfer files and for apps that support file sharing - you can use iOS file sharing with iTunes on your computer.
iOS: About file sharing.
http://support.apple.com/kb/HT4094
You should be able to email jpg files and then save them in the Photos app on the iPad.
GoodReader is one app that allows for some file structure. I do not use it and don't know much about it. You can check it out here and in the app store as well.
http://www.goodreader.net/goodreader.html