First up: Mendeley

First up:


I'm starting with this program because i'm currently using it on a daily basis for my thesis.

focus on Mendeley.

In the first screenshot you can see how the interface looks like on a mac, on windows is quite the same just blue colored instead of graphite: clean and intuitive.

The interface is tabbed: the first tab will always be the "my library" tab the others tab will be show pdfs in mendeley's embedded viewer.

Let's concentrate on the "my library" tab: on the left we have a split pane, in the lower part you can select some predefined filters(i.e. authors, tags and so on), in the upper part you are presented with three sections.
  • My library: quite self explanatory you can add folders but no smart folders, favorites and so on
  • Groups tab: quite a sexy feature i will explain that later
  • Trash: every deleted document will be there, you can restore them later or empty trash forever
The search bar in the upper right corner will let you perform deep searches even inside your pdf, keywords tags author and so on.
Focus on mendeley groups feature.

 If you share papers with your team groups is a key feature.
 You can create public or private groups to share papers with: all you have to do to share them is drag and drop from your library.
You and your team will then have a shared library, if you place a note in a shared paper it will show who wrote  it and when, with is perfect for a collaboration environment.
You can also select in the group setting if you want to sync only the references or the pdfs.

Papers in the cloud.

Mendeley free account gives you 500 MB of free shared web space  for your groups' papers, but also a 500 MB for your personal account.
You can also access you mendeley database either from your iPhone, mobile device or web browser  no additional costs involved.


Mendeley can also export and sync to bib latex but it will make a mess if you export/sync all of your library and collection into one bib file. (mess means  duplicate and such.)
I myself prefer to sync each collection to his own .bib file, much more clean and organized.
Right-clicking a reference in your library gives you the option to copy the latex citation key, very handy at times.

Mendeley it's able to import most of the common reference software bibliography formats, you can clip references from major scientific portals (e.g, web of science, science direct, scopus .. )
Lastly you can import papers from your disks, and compare them with google scholar to finish up all the reference details.

Though it has all of these great features it has of course its drawbacks.

 I'll start with minor and maybe personal gripes. 
It has no color coding, while it may seems a bit ridicule at times color coding can save you a whole lot of time.
Embedded pdf reader can be glitchy at times, especially with the highlighter tool.
Lastly sync process is non "automagic" and sometimes it just hangs up.
Web clipper is not polished enough.
Pdf can be matched only with google-scholar; even tough g.scholar is great a better option would be the possibility to choose from more services. 
No smart folders, they can be very useful.

All in all Mendeley is my favorite reference manager program for its multi platform and free nature.