The NSTA Reports December 2009 issue had some great resources for using and organizing science notebooks.
Science Notebooks in K-12 Classrooms has lots of notebook templates, examples of student work, and other resources for teachers.
Using Science Notebooks is a resource from Tucson Unified School District. Their site has suggestions for using science notebooks, the benefit of using notebook, examples of student work, and other resources for teachers.
The Scientist's Notebook Toolkit is a resource from the East Bay Educational Collaborative in Rhode Island. This site has a variety of resources including templates, examples, graphic organizers, and articles supporting the use of notebooks in science class.