Okular is a fantastic application to use for viewing and annotating documents like PDF and ebooks.
$ sudo apt install okular
It supports viewing a whole bunch of formats for viewing: PDF, DjVu, EPUB, TIFF, CHM and other ebook formats.
By default, the backends for the non-PDF formats are not installed. To get them:
$ sudo apt install okular-extra-backends
There is full zoom-in, zoom-out, continuous or separated page viewing options.
Table of contents are shown for ebooks, PDF and DjVu files that have it.
Thumbnails of current and neighboring pages can be viewed.
Okular uses a printing backend that is different from the one used by Evince, the default document viewer in Ubuntu. So, if you have printing problems in Evince, try Okular.
Annotating documents by adding notes, highlighting and freehand is easy.
Tried with: Okular 0.19.3 and Ubuntu 14.04