Ionic liquids have become a green media for engineering applications due to exceptional physicochemical properties, such as their practically nonvolatile nature, null flammability, low melting point, high ionic conductivity, and thermal and electrochemical stability. This work aimed to select the best fluorinated ionic liquids for the following applications: recovery/recycling of perfluorocarbon contaminants such as greenhouse perfluorocarbons gases and perfluoroalkyl acids of industrial effluents that are persistent, bioaccumulative, and toxic, and the partial or total replacement of inert perfluorocarbons in oxygen therapeutic emulsions by enhancing the emulsion stability and increasing the solubility of respiratory gas. With this dual goal in mind, thermodynamic and thermophysical properties of fluorinated ionic liquids (FILs) and their toxicity and biocompatibility are discussed so that the feasibility of the proposed applications can be evaluated. Herein, FILs are defined as ionic liquids with fluorinated chain lengths equal or greater than four carbon atoms. This paper provides a critical review of the experimental data for fluorinated ionic liquids available in the literature, and subsequently, with the aim of expanding knowledge of FILs, eight new fluorinated ionic liquids were selected for characterization. The attained results will clearly impact applications using polyfluorinated compounds.