Scholar's Toolkit

Publish or Perish is a software program that retrieves and analyzes academic citations. It uses a variety of data sources to obtain the raw citations, then analyzes these and presents a range of citation metrics, including the number of papers, total citations and the h-index. Available for Windows and macOS.

Zotero is an open source project. Use of the Web site and desktop application are free. Storage of files (PDF, txt, rtf, JPEG, and more) is limited to 100 MB for free accounts. There are additional options for purchasing storage. Zotero allows the researcher to organize and store more than just PDF files. It can also capture images, audio files, Web site snapshots, video, and text files. It also indexes the full-text of your library making it fully searchable.
 Review from Charleston AdvisorDownload Zotero Desktop (Windows, Mac, Linux) Install for iOS

Owned by Thomson Reuters, EndNote is one of the original citation managers. Not free, though does provide academic pricing. Very configurable with downloadable filters, styles and templates to aid in managing your citations and PDFs.
 Download EndNote Desktop (Windows, Mac) Install for iOS.

Papers was originally a Mac-only program, and the beautiful interface testifies to that heritage. Now owned by Springer, it costs $3/month after a 30-day trial, but now offers interfaces for all platforms and the web.
 Download (Windows, Mac) Install for iOS. Install for Android

EasyBib is an intuitive and affordable online citation and research management tool that allows for a complete research experience. In addition to its citation features, it also provides note taking, paper writing, and topic search features. However, the easy to use Autocite feature is probably its main attraction. EasyBib offers both free (MLA only) and subscription versions.
Review from Charleston Advisor

RefWorks is a web-based commercial program. RefWorks integrates well with many library databases, allowing you to easily import citations as you find them.

 Review from Charleston Advisor

Use of the Website and desktop application are free. Storage of PDF files is limited to 1 GB for individual users with a free account. An individual can choose to purchase 2GB ($4.99), 5GB ($9.99), or unlimited storage ($14.99) for a monthly fee. Mendeley invites users to not only house citations and PDF files, but also to create a network of contacts that can be followed, or to create a group with whom users can share citations.
 Review from Charleston Advisor  Download Mendeley Desktop (Windows, Mac, Linux)

Want more?!? Wikipedia has a page comparing features of more reference management software than you knew existed!