I have many pdf books, and I want to get them managed like a book shelf, but I can not find a good software on linux for such pdf management.
Maybe a firefox like "bookmarks" management will be enough, but acroread does not provide this.
Zotero is a firefox plugin that manages citations and references sort of like endnote, except that it can also store snapshots of webpages and actual pdf files.
It also has built in bibliography export functions that can output bibtex files, interface with endnote, and openoffice.
The front page of their website has a short demo-video showing how it is web-site aware and can pull bibliography information directly from amazon, googlebooks, jstor, and other websites. Pretty good research tool.
I use it with bibtex/latex myself.
Calibre claims to be the one-stop solution for all your eBook needs.
Calibre is freeware (available for Windows, Linux, Mac).
and a bit off topic: as for "managed like a book shelf", there is Bookshelf, one of the countless Russian eBook readers that does exactly that, unfortunately it's Windows only and only supports TXT.
speaking of Russian eBook readers (some of them are quite excellent!), here are 2 representatives that work for Linux (neither one supports PDF though)
FBreader supports TXT, HTML, Palmdoc, RTF, MS Word, CHM, zTxt, OEB, FB2, OpenReader
CoolReader 3 supports FB2, TXT, RTF, TCR, HTML, EPUB
all programs are freeware.
Check out eKitaab for eBook management:
eKitaab is free and open source software, it runs on Linux, Windows, and Mac.
Another option is Alexandria:
Alexandria is also free and open source.
Not strictly speaking an 'ebook manager', but I find tracker very useful for managing & finding all kinds of stuff. It's lightweight and very fast. It supports full content searches and allows you to tag documents.
The nice thing about this is you might find it useful beyond an ebook manager.