The development of educational applications has always been a challenging and complex issue, mainly because of the complications imposed by the cognitive and psychological aspects of student-computer interactions. This article presents a methodology, named We!Design, that tries to encounter the complexity of educational applications development from within the participatory design framework. The methodology enables computer literate students and designers to cooperate in the design of applications that (1) enhance typical educational processes for which students have extensive experience in, such as note taking or assessment, and (2) are well-suited to the technological, social and cultural particularities of each educational environment. The methodology can be easily applied in real educational contexts and consists of two phases. During the first phase, students participate in short-duration design sessions where they formulate needs, tasks and interface prototypes for the educational application under examination. In the second phase, the designers systematically analyse and then integrate student suggestions. In order to evaluate the methodology, it was applied in the design of two educational applications: an electronic assessment environment and a course website. A total of 86 undergraduate informatics students participated in 22 4-hour design sessions. The methodology was evaluated by collecting students' responses through questionnaires and by introspection on the video recordings of the design sessions. The design sessions proved to be a very intriguing experience for the students while the methodology's products managed to respond to their personal needs and expectations in an efficient and effective way.