EndNote is probably the most popular software in this area, for its accessibility to both Windows and OS X platform to some extent, while I am not the one who is crazy about EndNote because I am only in Linux, especially for Red Hat or CentOS. To be honest, EndNote is a user friendly tools with colorful interface, and it is easy to handle your reference of almost all disciplines through it. But you have to notice that it is not a free service, which may cause a little problem for students. In short, if you have no interest in computers and its development but dollars, go and get it.
She is my ideal lady. ResearchGate origins at May, 2008, an Olympic year. It is unique due to social network specialty, which means you can meet and discuss with researchers around the world. Moreover, it is a free software for scientific practitioners only. When you register, you are demanded to type in an email address from a institution or university. For most of you, it is not a problem. However, some odd universities including mine do not endow their student an official email account, even you are a PhD student. It is claimed that ResearchGate have more than 8 millions users now.
Mendeley is my boy, for I am not an authorized user of ResearchGate. An advantage of it is all-platform applicability, no matter you are a user of Windows, OS X, Linux and even ios & android. The registration is simple, an email address and a password are needed. Mendeley can scan and import your documents automatically after some configurations, and you can import from Google Scholar either. In addition to that, you can search authors by name, regardless of the original name of the pdf name, which is usually some unrecognized numbers and characters.
Other useful tools, such as PubMed, JSTOR, JabRef, Academia and etc are also recommended. Maybe I will update in detail some day. You can leave a message to have a discussion with me.