Sometimes you may want to write directly on a PDF in addition to creating notes about it in Zotero. These tools will allow you to do this (and you can always print out a clean copy of the original PDF (without markup - annotations, stamps, etc) if you need to).
Note: this listing does not include tablet apps such as iAnnotate, PDFExpert and GoodReader (all iOS) that enable you to annotate PDFs and other documents. These apps (including PaperShip) can sync with Zotero using ZotFile or the browser version of Zotero on your tablet (see the Mobile Devices tab on this guide).
Second Note: Not all PDF annotations are searchable! First they need to have been created by an application that follows PDF standards; second, in my testing it seems that an annotation that can be selected can be searched, but if its a mouse-over annotation, it can't. You will also see a difference in which annotations are viewable based on whether you are opening a PDF in a standalone app versus (the more limited) in-browser view. Be sure to test our your PDF annotation tool to see waht it can and cannot search.
You can always just take a camera/smartphone/tablet photograph of the text you are interested in and attach it to a Zotero record (by dragging it or using the paperclip), but these apps allow you to take a photo of that text with your device which will then be converted to a searchable PDF for you to attach.
Zotero can search inside attached files that are certain file types, notably OCR'd PDFs (note, you must install the PDF indexer in the Zotero preferences for this to work). To me, this is the real killer app for Zotero: it creates the database of you. Converting non-PDF documents to PDF makes them searchable. If you copy an article from a print source it will be an image file that is not searchable. Run it through Adobe Acrobat Professional (or convert it with a similar tool) and now it is a file that can be indexed and searched witin Zotero. Mobile apps on your smartphone or tablet make it easy to capture great pages or paragraphs in a book or article (just besure to also capture the citation! ;-).
What about articles that you receive from Interlibrary loan? Here at WSU, at least, ILL'd articles can be searchable PDFs or flat PDFs that are flat image files and not searchable. Your options for a image PDF are:
OCR - Optical Character Recognition.
Adobe Acrobat Professional: AAP is available at the WSU Libraries Creativity Stations (in the Dimensions Lab @ the Holland and Terrell Libraries, also at the Owen Science Library and the Animal Health Library).
Adobe Pro XI (or an updated version) is available from thinkEDU.com/BN at a greatly reduced price for WSU students (along with a bunch of other cool software). Be sure to also check out the Tech Store in CUE 305, or online at your My WSU student page (under Quick Links) for other discounted software.
Google Docs - Upload your file to Google Docs then download it as a PDF and upload or drag it into Zotero. Note - you must convert it to a Google Doc, and there is a 25 mb limit on files that can be uploaded and converted.
Libre Office - save a file in PDF format (you can also do this with Microsoft Word if you have Adobe Pro (or other iteration) installed)
Note: I have not vetted any of the tools below. Remember if you use a service that uploads your file to convert it, your file is stored on a strange server temporarily - so don't use it with anything that is private!
Mac Software (working on this...)