The following websites were helpful to me when I was applying to graduate schools.
Grad School Application Advice - Katherine Sledge Moore's website is similar to this one (in fact, it inspired me to do my own -- not to compete with her, but to show my appreciation for how helpful her advice was). She is a PhD student in psychology, so her experiences are a bit different from my own, in neuroscience.
PHDS.org - A great resource not only for the customizable graduate program rankings, but for the discussions on getting into graduate school and succeeding in graduate school that can be found linked on the sidebar.
National Doctoral Program Survey - Graduate school rankings by the National Association of Graduate-Professional Students (conducted in 2000, so may be a bit out of date, but I'll just mention that my program is #3 for neuroscience!).
applying_to_grad - A LiveJournal community dedicated to applying to graduate school. If you have a LiveJournal account, you can join the community to post your questions and participate in the discussion with other applicants.
who_got_in - Another LiveJournal community, useful when your applications have been sent and you're waiting to hear back from schools. Other applicants post when they hear back from different programs.
The Grad Cafe - Another site where applicants post when they hear back from programs. There is also a discussion forum where you can post your questions and join the conversation about grad school.
Yuster - Similar to The Grad Cafe, allows you to "track" individual anonymous posters to see where else they applied and which schools accepted/rejected/wait-listed them.
Please feel free to suggest additional resources in the comments!