Perhaps the most obvious limitation is Reader's inability to save modifications to a PDF file. Rest assured, this is the way it's supposed to be. Bryan Guignard explains what situations are appropriate for Reader, and when you'll need the full product.
Gordon Kent explores PDF forms, with working examples and step-by-step descriptions of how to populate a PDF file's form fields with data processed by a webserver. One example uses Microsoft's Active Server Pages (ASP) to populate a PDF form, and the other uses the ActiveX version of the FDF toolkit to populate a PDF form with data submitted from an HTML form.
Getting started with using Acrobat Forms. Gordon Kent explores how you go about setting up PDF forms on your web site: easy ways to get data from your online Acrobat forms into a web-served database, resent as email or other common applications.
OK, so you want to stamp your document. Maybe you need to give reviewers some advice about the document's status or sensitivity. This tip from author Ted Padova demonstrates how to add stamps with the Stamp Tool along with related comments.