A very powerfull and "mousepusher" tools is Scribus. A Opensource Desktop publishing program (like InDesign). Made for setting thesis and other Pages to be published (even presentations) It is powerful but needs some time to get a feeling. Here you choose where is text where are pictures and how things are set. http://www.scribus.net/ Disadvantage here, while most reference programs work together with both office suites and Open/libre office even brings its own reference manager with it scribus is needs some external plugins to manage referencesFor a scientist on the long run Latex is the better choice for long documents. The new suites make using latex easy and fast. Some advices here:
Both have an inbuild BIBTEX editor (how to manage references). However sometimes it is just nice to do this externally with jabref (see section refmanager)
Many cooperators still like to use word to write papers, to oblige them
you don't need to convert the original Latex into word but you can convert
the final pdf including the formatting.
This script worked for me very well: https://github.com/dothinking/pdf2docx
At Lund university we have a cite license to PDF-X. See https://program.ldc.lu.se/Download
Reference managers can do much more then just make the reference list in
the document. They can collect your PDF and keep them sorted and even
more, you can write notes in them, comments to the paper.
Jabref and docear have the advantages that they are based on a singe file and can put the file links relative to this file. That means you can have your whole database on cloud services or a usb stick and are independent.
Build into many of the tools are the automatic extraction of
bibliographic informations from e.g. the DOI or the ISBN There are however
specialized tools available that perform these tasks too.
This webpage creates a citation from the ISBN http://www.ottobib.com/
This webpage creates a citation from the DOI https://www.doi2bib.org
Mendeley has a need import feature. It reads in the PDF’s and analysis them. It’s free in its basic functionality, if you store files in it (which you want) than it will cost you at some time. A need function is the sharing with other people. I was acquired by elsevier. It works in Microsoft and Openoffice/Libreoffice and synchronizes to bibtex http://www.mendeley.com/ I found the exporting function to be bit buggy, but in general a nice program
For bibtex files, there is a nice free java based reference manager
called Jabref. https://www.jabref.org There
is a new plugin for Word available that offers similar features to Endnote
and the other mentioned (see below). It now has automatic import features
from ISBN or DOI. I usually get a citation with DOI into the program.
Important you can link all your PDF (an rename them) and give a relative
path to the bibtex file. So I use Dropbox and synchronize all my files
with it. It has a neat group function that allows for sorting of
references into groups and then you can choose multiple groups to limit
your vast library. My go to program.
The word citation tool now works very nicely. Find an instruction here: http://www.ee.ic.ac.uk/hp/staff/dmb/perl/index.html
We (Lund University) have Endnote and an old version of Reference manager in the department for free.
Openoffice/Libreoffice has it’s own reference manager.
If you write with LATEX, you could of course write the references in the file by hand and use a formatting tool. The better choice however is to collect the references in a so-called bibtex file
a need thing for bibtex is this cleanup tool: http://bib-it.sourceforge.net/
just stumbled over this useful tool. It extracts a library from a word document and makes a new file out of it. highly recommendable https://rintze.zelle.me/ref-extractor/