We just added a page of resources about making accessible documents using Adobe InDesign, which is widely used to create professional print and PDF publications.
It is always best to make a document as accessible as possible using the application that created it before converting it to PDF! You'll find it much faster and easier to make an accessible PDF when the source document already contains the features you need, and if the PDF ever needs to be replaced with an updated version you won't have to re-do most of your accessibility work.
Visit Making Accessible InDesign Documents for links to documents, videos and online courses on this topic!
For information on creating accessible documents from Microsoft Word, PowerPoint and Excel, please see our learning package: Design Accessible Documents.