Nature Reviews: Cancer has published a very cool "subway map" of known molecular pathways involved in cancer. Specific genes in each pathway are shown as subway stops, and the major cell phenotypes required for cancer are "main stations" on the various lines. Each gene on the map has a link to a detailed description on NCBI's LocusLink, and the authors have also written summaries of each cell phenotype/pathway (the "main stations"); both of these are found by clicking on the gene/station name (note: this only worked in IE for me, not Firefox). The "main station" descriptions make a good starting point for exploring the map. (via BoingBoing)
This map reminds me of a class I took in graduate school where our entire goal was to look at all the proteins and other elements involved in one of the heat shock pathways and analyze the interactions between them. On the first day of class we got a rough draft of a regulatory diagram much like the subway map above, and then spent the course trying to improve it based on primary literature and logic. What made it really enjoyable was that this wasn't an exercise where a better diagram was already known; the draft diagram we had was the best information the instructor had at the time.