[1][2] In the 1970s Goguen's work was one of the earliest approaches to the algebraic characterisation of abstract data types and he originated and helped develop the OBJ family of programming languages.

[2] Goguen's research interests included category theory (a branch of mathematics), software engineering, fuzzy logic, algebraic semantics, user interface design, algebraic semiotics, and the social and ethical aspects of science and technology.

[3] Goguen's research with Thatcher, Wagner and Wright (also in the 1970s) was one of the earliest works to formalise the algebraic basis for data abstraction.

[4] In the early 1990s Goguen and Rod Burstall developed the theory of institutions, a category-theoretic description of logical systems in computer science.

[18] Goguen also studied the philosophy of computation and information, formal methods (especially hidden algebra and theorem proving), and relational and functional programming.

[5] During the late 1970s and early 1980s, he was a faculty member of the science program at the Naropa Institute in Boulder, Colorado.