Microsoft Excel remains a popular tool for managing systematic reviews. One source of excellent templates for Systematic Review record-keeping is available from the library of the UT - Austin School of Public Health.
From the Center for Evidence Synthesis in Health (CeSH) here at Brown University. Software for (semi-automated) abstract screening for systematic reviews. At present, abstrackr is a free, open-source tool for facilitating the citation screening process. It allows for collaborative screening of abstracts, and is set up to automatically pull in abstracts from NLM using PMIDs or transfer abstracts from Reference Manager or EndNote.
Abstrackr is currently integrating machine learning technologies to semi-automate the screening process. Already, abstrackr will prioritize the screening of those articles most likely relevant to the review at hand. In the near-future, it will screen out irrelevant citations for you, automagically.
Covidence is a not-for-profit service dedicated to improving the use of evidence in healthcare decision-making. The interface is easy to use. There is a free version for small reviews, and a fee structure for larger projects.
EndNote is citation management software that is free to Brown faculty, staff, and graduate and medical students. With EndNote, you can: import references directly from multiple databases; organize and manage references; and format bibliographies and manuscripts.