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The paper focuses on experiences gained during the last years with the WebCT virtual learning environment together with multimedia applications supported education of three subjects. WebCT has been used at the Faculty of Informatics and Management since the beginning of this century. The author of the paper has been prepared with her students various multimedia applications dealing with objects appropriate to subject matter for more than 15 years. In the paper we discuss a benefit of multimedia applications and utilization of the WebCT courses used as a support of subjects dealing with graph theory and combinatorial optimization, i.e. Discrete Mathematics and Discrete Methods and Optimization. The paper also mentions the WebCT course prepared for the subject Algorithms and Data Structures aimed at the development of students' algorithmic thinking essential for the mentioned subjects.