You cannot go wrong choosing any of the tools, but it helps if you take a few things into consideration before starting. Remember that you can switch between the tools, it just becomes less convenient the longer you use a tool and the more file attachments you collect.
Reasons to choose EndNote:
Zotero and Mendeley are relatively young tools when compared to EndNote. EndNote offers some advanced features that might be necessary for your discipline and work flow. The University of Lethbridge has an institutional subscription to EndNote, so you have access to it as long as you are affilitated with the U of L. We also provide regular training sessions on it and a fair amount of institutional support. Even if you no longer have access to the subscription version of EndNote, you can still access EndNote web in the 'cloud'.
Reasons to choose Zotero:
Your research content is diverse: It is the easiest method to gather citation records for non-PDF and PDF content. Zotero's single-click capture works with more databases, catalogs, and websites than Mendeley's Web Importer. You can also enable the retrieval of PDF metadata, which allows you to create citation records just from dragging a PDF into Zotero. Zotero is open source and cannot be acquired by a company.
Reasons to choose Mendeley:
Your research content is primarily contained in PDF files: Mendeley has an integrated PDF viewer and can create citation records just from importing a PDF file. Mendeley.org has the strongest website and community platform, and is as much a social network for academics as a citation management system. Mendeley is owned by Elsevier, and links well to articles in ScienceDirect. A basic account is free.