As you consider which PDF annotation software may work best for you as a researcher, remember to make sure that it works with the devices you use and with the cloud storage platform you use. If you use a mobile scanning app (more info via WSU libraries' guide), you will want to consider if the scanning app creates a PDF you can annotate with the options listed below:
Foxit Reader [Free to $] - use on your computer as well as your mobile device (Google Play / Apple).
Adobe Acrobat Reader [Free to $] - use on your computer as well as in your browser via Adobe Reader commenting tools (guide on how to enable in your browser from OSU). There is also a free mobile app (Google Play / Apple).
PDF Annotator ($) - works with Windows
PDF-Xchange [Free to $] - works with Windows.
Xournal++ (open source - Free) (Windows / Mac / Linux) Xournal++ is a handwriting notetaking software with PDF annotation support. Written in C++ with GTK3, supporting Linux, macOS and Windows 10. Supports pen input from devices such as Wacom Tablets.
iAnnotate PDF (iPhone / iPad) ($)
Use to annotate and read PDF files on Apple's iPad.
Flexcil (iPad only - free to download, in-app purchases)
PDFescape (free to $) Works within most browsers as a PDF reader/annotater. Also offered ($) as a download for Windows (more info on installation).
PDFViewer (Apple - mobile/Mac & Android) Annotations, forms, signatures, document editing and sharing, all in one, free package.
PDFExpert (iOS) (helpful page on using PDFExpert with Box) (free to $)
GoodReader (iPad, iPhone, iPod Touch) (user manual)
Hypothes.is (open source - free & works in your web browser) You can share annotations & highlights with a public Zotero group using Zocurelia (here's the form to create the group). There's also a project on GitHub that will import your notes in Hypothes.is into Zotero (with their tags) - please note, I haven't tested this yet.
More info on the iPad & PDF Annotation software