PDF versus EPUB: Comparing ebook formats

Conclusion: If you’re reading technical books or doing research, opt for PDF. If you’re reading fiction or casual nonfiction, EPUB will suffice. Use BookReader to convert EPUB to PDF, where necessary.

PDF Format
+ Designed for print fidelity: enables sophisticated page layouts
+ Supports annotations (highlights, comments) on layer above page content
+ Keep annotations packaged in PDF itself
+ Large selection of capable PDF reading & annotating apps across platforms
+ Easy to convert any ebook or document to PDF
+ Very popular: PDF is the preferred format for sharing technical, business & legal documents
- Usually suited for large displays such as retina iPads or laptop/desktop screens
- Very few online stores offer DRM-free PDFs
see also: Extracting Knowledge from PDFs using PDFoo on Mac OS X

EPUB Format
+ Allows flowable text, changing fonts & text appearance
+ Built on web technologies, supports interactive HTML components
+ Great for reading on mobile devices with small screens (less than 8 inches)
+ Emerging as a popular format for ebook stores
- No built-in support for annotations, proprietary feature provided by EPUB readers
- Limited annotation capabilities provided by EPUB readers
- Concept of “page" doesn’t exist since text is reflowable and fills the display as specified
- Difficult to reference a particular location in the ebook from your notes
- Few EPUB readers, lacks cross-platform EPUB reading, markup. and sync solutions
see also: Best EPUB Reader on Mac OS X.