What is the fate of sulfur in cysteine when it participates in gluconeogenesis?
Cysteine is a dispensable amino acid required for synthesis of protein and non-protein compounds. These non-protein compounds include pyruate (hence acetyl coenzyme A), taurine, sulfate, and glutatione (GSH). The fate of the cycteine is hence sketched in following diagram (Ref.1):



As evidence from the diagram, the sulfur atom in cysteine has been converted to sulfate ion ($\ce{SO4^2-}$) through $\ce{HS-}$ ion. This fact has been previously proved experimentally (Ref.2). Accordingly, the first major step in cysteine catabolism in mammalian tissues is the oxidation of cysteine to cysteine sulfinic acid catalyzes by cysteine dioxygenase (CDO). The reaction mechanism of this non-heme iron dioxygenase has been recently reviewed (Ref.3).

References:


G. Courtney-Martin, P. B. Pencharz, “Chapter 19: Sulfur Amino Acids Metabolism From Protein Synthesis to Glutathione,“ In The Molecular Nutrition of Amino Acids and Proteins; Dominique Dardevet, Ed.; Academic Press, Elsevier Inc.: London, United Kingdom, 2016, pp. 265-286 (https://doi.org/10.1016/C2014-0-02227-7).
Catherine L. Weinstein, Rudy H. Haschemeyer, Owen W. Griffith, “In vivo studies of cysteine metabolism. Use of D-cysteinesulfinate, a novel cysteinesulfinate decarboxylase inhibitor, to probe taurine and pyruvate synthesis,” The Journal of Biological Chemistry 1988, 263(32), 16568-16579 (http://www.jbc.org/content/263/32/16568.full.pdf+html).
Crisjoe A. Josepha, Michael J. Maroney, “Cysteine dioxygenase: structure and mechanism,” Chem. Commun. 2007, (32), 3338-3349 (DOI: 10.1039/B702158E).