I'm using Mendeley Desktop. Is easy and has a lot of features.

Also you can use if you're writing your thesis using MS Word, MAC Word, OpenOffice or BibTeX.

I prefer EndNote. After some changes the incorporation in Microsoft Word is now OK.

If you write your thesis with LaTeX, some of my friend have good experience with JabRef.

The doctoral students in my group use ENDNOTE and they are very happy with that.

Endnote X6 is very nice... you can save your library on your own account on the website and synchronize continuously, so you can use it anywhere from any computer..moreover, Endnote can be downloaded on iPad..

I have been using Endnote X6 for quite a while and it is very easy to use and satisfies almost all the requirements of thesis and manuscript writng.

Used Reference manager 12.. I like it.. as u can directly do internet search through the application itself and insert that references into ur word document !

I really like Mendeley,, it is free, it has a lot of reference styles, you can import or export you library to endnote, etc.

I believe that Endnote is hard to beat. It is on the web, on the Mac, Pc and the Ipad version is great! It works perfectly with Word.

Papers, really nice interface, easy, efficient, intuitiv, work for MAC and Windows.

I am using JabRef for publications and my theses (diploma, PhD). You have to get used to the interface, but it is nevertheless a nice little tool. Works best with LaTex, of course. However, there are ways (e.g. BibTex2Word) to use it with Word, too.

http://jabref.sourceforge.net/

I recommend Papers2 by Mekentosj - which is available for both windows and osx. By the way Mekentosj is now part of Spinger. http://www.mekentosj.com

Papers2 works great with word, pages and latex.

I am using Mendeley since it is multi-platform compatible and got LaTeX-export and quite simple and clean sorting and pdf-reader features. It automatically syncs all pdfs to all your devices, including iphone and ipad!

Endnote is definitely the best choice when it comes to designing your personal citation style very easily.

I heard good things about Citavi though.

hi Seda

we use from Endnote

I have been using EndNote X4 for a while and have compared it to open-source reference managers like BibTex or JabRef. In my view, EndNote is hardly beatable, it just makes magic when it comes to managing your references. So, if you can spend USD 249.95 on a reference manager (EndNote X6) , I will undoubtedly suggest EndNote. Nonetheless, BibTex and JabRf are pretty decent reference managers and, most important, they are available for free and you can combine them with DOCEAR, an "academic literature suite" which is incredibly helpful when it comes to write papers (www.docear.com) . By the way, EndNote people made the HUGE mistake of sueing DOCEAR for having included EndNote among compatible reference managers. They could have gained a lot by keeping that compatibility available. Crass error!

Zotero

PyBliographer

JabRef

I use EndNote X6. Its the best :)

Thank you guys. I have an idea now...:))

Endnote X6...

endnote x6

Mendeley for LaTeX users is good

Endnote also!

"What else?" (Georges Clooney)

Mendeley

End Note X5!

I would use Papers. It is very simple, especially on a Mac and also interacts well with iOS devices, such as the iPad. You can also easily store the PDFs and have them in a clous, so they download to other machines/ devices.

Both endnote6 and mendley are equally good..

Mendeley reference manager and PDF organizer is the best for thesis and paper writing

Mendeley seems to be free. I am downloading it as I type.

Thanks to all those who spoke of it.

Mendeley is interesting and useful. Moreover, it has Microsoft Office plug-in, you can use references collected in Mendeley directly in the Word...

I have read very positive opinion about LibreOffice (free word processor) and its capacity as reference manager, but I didn't verified it...

EndNote

Mendeley is equally well integrated in LibreOffice as it is in MS Office. Mendeley sports some very useful features, such as peer-to-peer web-based article search, automatic addition of .pdf files into the library using the document's metadata, removing duplicates from your library, etc. I haven't had any problems running it on Windows7 or Ubuntu, ànd it's free... I think there is little more to ask for...

Endnote

Reference manager 12

Endnote

Endnote 6

End note 6

ENDNOTE

JabRef

ENDNOTE or REFWORKS. I 've tried the both tools with the same efficiency.

endnote

With due respect, I am worried. You go to Harvard and do not know what ref. manager to use? Which one do your fellow colleague scientists use to write their papers?

You would be amazed what people do in real life. My colleagues curate their manuscripts/thesis/project bibliographies *by hand*. Yes. Copy/Paste, look where the reference was cited in the manuscript, change the number... You removed a reference? Go back to the manuscript, shift numbers upwards, modify the reference section... You added a new reference... You know the drill. Mind-bogglin.

Zotero

Menedely, it is FREE and high quality. It works as a desktop application but all your pdfs are synchronized on-line so you can access them from any computer with an internet browser. Mendeley can export citations in many formats. You can share several folders with collaborators. You can see a review from MIT http://libguides.mit.edu/content.php?pid=55486&sid=427307

It is possible to notes within the pdf, highlight text etc.

I use Mendeley, it takes short time to learn how to use it.

End note or Mendely. I never liked End note though, but Mendely is both free and super easily to use. However, it lacks some citation styles that you could only get through End note.

I use Mendeley. I write my papers in IEEE format and i find it is precise in its reference formatting. I have also recommended it to several friends who are using it for Harvard referencing. Again, it is accurate in its construction of their references. Mendeley also stores your documents online, so they are accessible across various computers and also cross-platform. It's also available for andriod. I started using Refworks, but i found it more restrictive than Mendeley, partly due to its need for a network or internet connection. Overall both systems provide the same functionality, although Mendeley is free.

End note

End note

I am using here END NOTE its better

I use Jabref

Hello, I am the founder of Docear which is a free and open source literature management software for Windows, Mac, and Linux. Docear has a unique concept that helps you organizing, creating and discovering academic literature with a strong focus on the management of PDFs and annotations.

If that sounds interesting to you, have a look at http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/

And you might also be interested in this article which is discussing some aspects of how to (not) chose a reference manager http://www.docear.org/2013/10/14/what-makes-a-really-really-bad-reference-manager/

I think, it was not yet mentioned here: Citavi. I prefer this software as it is also a great tool to organize knowledge. In Citavi, you not just collect papers, but information (cites, figures, etc.). Additionally I like the concept of placeholders inside a document "{Author 2011}" instead of scripts as for example used by Endnote. 

Mendeley!

Looks like this qn was asked long back!  Bu yeah I used couple. Refworks currently..ref manager-used earlier and read cube too!For my purpose, all works great! Although readcube needs our subscription to synchronize between computers, refworks in that sense is better as it is all over the net!

Mendeley and EndNote.

Mendeley and R like this workflow

Mendeley!!

Seda, I use Mendeley with LaTeX for the reasons given in this publication

https://www.researchgate.net/publication/283831577_Step-by-Step_Procedure_to_Cite_References_from_Mendeley_and_Reference_Management_Software_in_LaTeX_Journal_Articles_Conference_Papers_Thesis_Dissertations_and_Research_Proposals?ev=prf_pub

Gerro

Technical Report Step-by-Step Procedure to Cite References from Mendeley and ...

To all those who might still be reading this old question and have doubts, I can only recommend Citavi. It is simply the best. I tried Zotero, Endnote, Mendeley and in the end Citavi.

And Citavi simply beats everything, at least it did 4 years ago in my opinion when I compared them. These programs have changed and gotten better for sure, but so has Citavi. But right now I'm still using Citavi from the beginning till the end of any scientific paper I write.

Let's imagine you want to study a certain topic and do scientific review about it.

You can search inside Citavi thousands (yes thousands) of databases. Pubmed, Sciencedirect, Wiley, Springerlink, Scopus, are just some of them. Is the database password protected? No problem, just insert your credentials. And you can search the databases you selected simultaneously if you want to. Including Boolean searches. And after you click on search, Citavi starts to list all the results, including bibliographic data, doi numbers and most importantly the abstracts, immediately, there, at your finger tips. Then you just select the ones you want to keep or just keep them all.

Then you can tell Citavi to fetch the fulltext, if possible. Or you add the paper manually, if you have it (or simply copy the doi number, insert it in a certain site, and get the full-text).You can also search Database sites themselves, or in case of web-pages let the pickers of Citavi import all the website data, and even save the web-page.

You then read the abstract or even the PDF full-text, underline it (and keep it underlined), and save these underlinings as citations, write your own ideas, schedule tasks for certain papers, whatever you want, it is there. You can search inside your abstracts (all of them or a specific subset) or inside your full-texts.

Then you organize these citations, this knowledge into subtopics (if you want to, but I strongly recommend it) and in the end you tell Citavi to show all these citations and ideas, in an organized manner, next to your word processor window, and you can begin to write. Papers almost get written by themselves this way, and always with the bibliographic source attached to it.

In the end you just tell Citavi to tidy up your paper with an organized bibliographic list at the end of your text, according to the citation style you want, or even according to a citation style you changed or created yourself.

Just try the free version (everything works as the full version, except the reference numbers are limited to 100) and see for yourself. If you need to organize more than 100, well, then you have to pay for it, but it is worth it. You can also tell the program to install itself on a USB thumb drive, and there you have it as a portable version on any computer.

If you ask the Citavi team nicely, tell them what you work is about, i.e. participate in the prize draw that the Citavi team does each month that , you might even get it for free. At least I did so, several years ago.

And no, I'm not a Citavi employee, just a guy very very grateful for its existence, and for making my scientific writings so much easier. There is a reason why Citavi is endorsed by most German universities, and every student gets a full license...it is simply the best.

I have used and liked mendeley, but for many versions the bug persists. I have stumbled upon this error last year, namely I have some problem syncing with cloud (the format in one record is invalid). The only help I got from mendeley team was to remove and purge the files and database locally and to download everything from the cloud. I could not afford such solution because it is too risky - I have some very important work to do. Hence I resolved to move to some open source solution. If mendeley was open it would have been surely repaired sooner...