When one looks back on his/her notes and memos taken before, the context information like what references were used is easily lost, and often hard to recreate. Reserving traces for such referencing, including references to others' notes, is expected to be highly beneficial for collaborative learning. We have developed a note-taking system, the ReCoNote or the Reflective Collaboration Note, to implement such record keeping. Notes are taken with mutual bi-directional links with explicit comments. The ReCoNote has been used in university classrooms successfully. The students gradually got used to the collaborative uses of links, and found several useful ways to use the ReCoNote to help themselves engage in more productive learning activities.