Researchers normally write papers about their findings to communicate to the public and the peers, and it is a general practice that when ever they write they should review the previous work on the subject (in Introduction and Discussion mainly), and correlate their results with previous works (in discussion part) and also base their methods on some previous references (methods part). So it is essential to “quote” some previous works. Thus it is needed that the writer (here the researcher) should have a systematic way to “quote” the previous works, and this practice is called referencing. The last part of the research communication normally holds a subsection called “references” or “bibliography”. It is generally a tedious process to arrange the references according to the publishers specifications, and there are many popular referencing styles like MLA, APA, HARVARD etc. Each journal publisher normally has a different referencing pattern or style, although I don't understand why they do it (I feel that it makes me more careful when I write a paper).
With the advent of computers and internet there is a chance that the researcher has his own bibliography library in *.pdf format in their Personal Computers. The researcher is also aided by numerous “referencing softwares”, like ENDNOTE, REFERENCE MANAGER, MENDELDY, JABREF, KBIBTEX, ZOTERO to name a few. Out of these, softwares like Endnote and Refernce manager is “paid” and researchers working in smaller universities or institutions or from poorer countries cannot afford them, some others who don't like “closed source” softwares do not use them!! So what is the way out, here comes the open-source free applications, operating systems etc. Firefox browser is one of the most popular open-source application used by everyone. In the field of referencing softwares the last four softwares that I mentioned above are free for everyone, and the last three are open-source.
I have used endnote, zotero and mendeley and plan to use the others sometime in the near future. Endnote is the GOLD STANDARD for referencing softwares and there are a lot of places to find details about them. Mendeley is a recent entrant to this field, and Zotero is a tried and tested software for the past few years. I intend to make a small reivew of my experiences about my referencing problems after the entry of mendeley into my radar!!!
Mendeley the next big thing in referencing!!
Once I started using Mendeley almost 8 months ago, I was amazed by the user friendliness that it offered, it was just like "the thing that I needed" for a long time. I could just add the PDF's in my hard-disk to it and it would create the bibliography, would organize the pdf's, and I could read the pdf's in its window!!! “MAgiC”. I read somewhere that it is similar to PAPERS a software for MAC OS. Everything was going well until I noticed a entry in the left hand side window called “NEEDS REVIEW”, so what the hell was that? So the “magic” was having some problems, how the hell did mendeley create the bibliography database when I just added the pdf's? The mendeley web site says that it scans the documents (pdf's) and get hold of some information like DOI, author names, title etc either one of them or all of them, search in google scholar or pubmed and create the database of “CITATIONS” that is how their API works. So here was the problem not all the pdf's would be recent, some would be scanned copies so the software gets some problems to extract the information from the papers to search the web. I have some examples of this “Siepel, A., Nielsen, R., R, R., Kosiol, C., & Vinar, T. (2010). Positive selection on apoptosis related genes. FEBS Letters, 584, 469-476.” so what is the problem here, the first author of this paper is that R, R. who is my colleague so everything has gone wrong with this reference there are many papers like this in my database (the figure above shows the problematic database that I have out of 1000's some 100's are problematic) So is the excitement going to end? No is the answer,
the developers are creating or working on updates and there will be a “fools-proof” software recently but not now it is still in its infancy. There are some related problems too but it does not matter to many people but is worth a mention here: 1) it is closed source 2) if you need to sync your pdf's on the server you need to PAY money, you are restricted to only upload a certain amount of 'bytes' of data to the server, so even if you have an exhaustive (I cannot imagine that amount of references alone) amount of references you will have to pay. 3) now the support for long and short journal names are missing (I read it somewhere I dont know what it really means but it is a problem :) )
My work-around
the developers are creating or working on updates and there will be a “fools-proof” software recently but not now it is still in its infancy. There are some related problems too but it does not matter to many people but is worth a mention here: 1) it is closed source 2) if you need to sync your pdf's on the server you need to PAY money, you are restricted to only upload a certain amount of 'bytes' of data to the server, so even if you have an exhaustive (I cannot imagine that amount of references alone) amount of references you will have to pay. 3) now the support for long and short journal names are missing (I read it somewhere I dont know what it really means but it is a problem :) )
My work-around
So what will I do? I am happy with the software, I can use it to organize my pdf's no need to open the directory every time to read the pdf's just go to mendeley and click on the citation and you will read the paper in their cool window.
What about a turn around to use mendeley as my reference manager and “cite-while-I-write” if it gives some erroneous references?
This is the method that I would suggest, if you really don't want to pay for ENDNOTE. There is a very very good application called ZOTERO, as I mentioned earlier, which I have used for a long time. It is actually a FIREFOX plugin. Once you open a research paper in your firefox window zotero recognizes that and there is a “page” symbol in the right hand side of the “address bar” click on that “MAGIC” automatically the citation is saved in your zotero bibliography database(see figure above how to save in zotero). If this symbol do not appear, go to the respective publisher page 
and there will be an option to “EXPORT CITATION” click on that, it will ask which format, click on any format like “ris” “endnote” etc. the citation will be saved in zotero library. Access the zotero library by clicking on the zotero button on the right hand side of your status bar of firefox, organize the database, and install the cite while you write plugin for zotero so that you can cite while you write in your favorite writer like MS office word, Open Office Writer, of Libre Office Writer. If needed select all the citations in zotero export them as a bibliography database in RIS or endnote RDF format (see the figure above on how to export from zotero) and IMPORT them to your ENDNOTE or MENDELEY and use that software to cite-while-you-write. Although I would prefer to use zotero to do that (see how I cite while I write in the figure below) and use mendeley to read my pdf's.
Zotero allows you to sync your databases, so you can open them in any firefox that you use in any computer in windows or linux, save new references anywhere and sync them and you have your database intact and accessible from everywhere. Another beautiful thing is that zotero now has a standalone version, if you don't want firefox use that, I have read that chrome now has zotero plugin (I am not sure about it since I don't use chrome now-a-days).
