There is no one citation management software that is objectively "better" than another. All of the citation managers listed here share the same basic functionality: storing and organizing bibliographic information, generating citations, integrating with web browsers and word processing software, and allowing for collaborations / group projects.
You will need to choose the option that makes the most sense for you. If you are collaborating with others and they are already using a citation management program, it would be a good choice to use the same system.
The Library supports EndNote Basic (formerly called EndNote Web), Mendeley, and Zotero.
Compare your options: Here's a good list that compares EndNote, Mendeley, and Zotero, created and maintained by librarians at Penn State University Libraries.
Or attend one of our Introduction to Citation Management workshops, offered each semester, for an introduction to all three and the chance to work with our specialists as you get started. The link below contains the workshops schedule for the current semester and includes a sign-up link for the citation management workshop.
EndNote has the greatest functionality (probably more than most researchers would ever need to use), but you have to buy the software. Visit the ISU Book Store for information on available versions and pricing.
EndNote Basic is cloud-based and free, though ISU affiliates have access to many more citation styles and more storage for files than non-affiliates. You can also share references with collaborators when working in a group. If you have both EndNote and EndNote Basic, you can sync them together. However, there is no need to have or use both - they are independent of each other.
If you frequently use Web of Science, consider using EndNote or EndNote Basic. Since Web of Science and EndNote are owned by the same company, they integrate seamlessly.
Mendeley also has both a desktop version (Mendeley Desktop) and a web version (Mendeley Reference Manager). Both versions of Mendeley are free, but some features require a premium (paid) membership. There is also a Word add-in called Mendeley Cite.
Mendeley's features are very similar to Zotero: you can drag and drop PDFs to extract metadata, create group libraries, and organize your references with folders, notes, and tags. However, public groups were recently removed from Mendeley, so if you want to create a public list of references, Mendeley is not a good option.
If you use the online version of Word or are a major user of Elsevier search tools (such as Scopus or ScienceDirect) and have an Elsevier account already, you may want to consider using Mendeley.
Unlike Mendeley and EndNote, Zotero is an open-source citation management program. Zotero exists as a desktop application, which connects seamlessly with Word, and a "connector" for each of the major browsers that allows you to gather citation information from the web. Zotero also does a fairly good job of pulling metadata (information about a source, which is needed to create citations) out of PDFs for you.
Zotero integrates very well into the most commonly used browsers for Windows, Mac, and Linux. It can collect better, more complete citations than the other options in some cases, especially from web resources. The latest versions of Zotero utilize Unpaywall to find free PDFs of articles and connect with Retraction Watch to flag retracted items. It can be seamlessly integrated into Word and other word processing programs such as LibreOffice. You can also use Zotero with Google Docs in Firefox and Chrome!
If you are interested in open source alternatives to the mainstream citation management programs, or are interested in a citation manager that works with Google Docs or can help you find free (and legal) versions of papers, consider using Zotero.