Academic texts typically use acronyms to refer to books in Tana"ch, Talmud, and rabbinic literature. I am presently working on editing the citations given within a translation to bring them more in line with academic standards. However, I have only been able to find abbreviations for biblical books and sha"s. Is there any resource for academic abbreviations for other sefarim in Rabbinic literature?
Try the preface of an academic-style book on Talmud. The better editions of the Jastrow dictionary have an abbreviations page that I believe covers Talmud Bavli, Yerushlami, and Medrash including some names and lots of academic abbreviations other than titles.