Sci2
Modular toolset specifically designed for the study of science; temporal, geospatial, topical, and network analysis and visualization of scholarly datasets at the micro (individual), meso (local), and macro (global) levels
PoP (Publish or Perish)
Calculates citation metrics from data in Google Scholar
Citespace
Freely available Java application for visualizing and analyzing trends and patterns in scientific literature.
Gephi
Open-source network and visualization software; import data from almost anywhere under-supported file formats. Requires knowledge of Java and/or OpenGL
Bibliometrix
Open-source R-tool that is used to complete complex scientific bibliometric analysis