For djvu files, I enjoy reading it in djview, because when I search for some words, it can show where all the results are at a glance, and highlight them simultaneously. This is much more convenient than the searching functionality in evince for pdf files.
For pdf files, I enjoy using Xournal to annotate it, for example, underscore some lines, add text comments.
But for a single file (pdf or djvu), I have to create two files (one in pdf, and the other in djvu) and open them in djview and xournal (and maybe also in evince), in order to achieve the two benefits I outlined above.
I haven't tried many other functionalities of djview, xournal and evince, neither have I tried many applications yet. Do you have some convenience ways to achieve what I hope to do and possibly more which I haven't mentioned yet?
My OS is Ubuntu 12.04.