Here is an excellent iPad in the classroom workflow description from wanderingacaddmic. These guys have put together an article that walks you through the process of Collecting, Annotating and Redistributing Student Work using an iPad, GoodReader, Dropbox (and optionally Jotform). I love the fact they have included the screenshots so I know I am doing the right thing that first time I go through this.
GoodReader ($4.99, iTunes) does a lot. It allows you access to all manner of cloud-based document servers, email attachments, locally saved files, and even S/FTP. It lets you view office docs, pdfs, images and multimedia files. It lets you zip files together, email from the app, or open the files in other apps for the purposes of editing. You can search within files, and most importantly for the present discussion, you can annotate files with drawings, highlights and sticky notes.
Use case: Collect work from students, mark or comment on it, send it back to them.
This is a fairly standard use case for teachers. Students have produced some work in the form of a document and you want to give them feedback. Here is the iPad workflow with some advanced tips.................