The American Historical Association has a directory to every doctoral program in the United States and Canada. If you look to the left of the page on the link provided, you can look at all of the programs either alphabetically, by region, or by department specialization.

Edit: If you have any other questions about the application process, let me know. I just got done with the PhD application process myself this past semester.

I'm at the other end of that process. First of all, figure out who's working in your subject or related subjects--for this, you will need to look at books and journals. So it's back to the library! Find one whose work is acceptably close, who is senior, who is with a top-20 doctoral program, and who seems to have good advisees who place well after completing. (edit: And, of course, who complete at all...)

Write to that person about your interest, and do so with some knowledge of their work and other assets in the Department. The reply will tell you hopefully what you need to know about whether you want to apply there. Some programs with excellent faculty in your particular area have terrible support or fractious politics, but even if not, you'll need that advisor to go to bat for you against the other great applicants in the pool. Be more than a name on an application--be a person to your potential committee; be someone they want to claim as their own. So don't look for programs first, but for people.

A good advisor and a talented cohort of fellow students can make graduate school a delight and renew your commitment to the craft--besides giving you a strong leg up in the job market through her or his reputation. Bad ones can crush your soul as you flame out. So first, find your potential mentor in the scholarship, and if they seem welcoming and are with a strong program, you've found what you need. Even if they warn you off, as I often have to do for potential PhD advisees whom our degree program can't do justice, you may get good advice regarding where you might find greener pastures.

(I give this advice both as someone who followed it, and as someone who tells their own undergrads and MA grads who want an academic track to do it. It's essential if you want to find a good program and actually get in even with a Berkeley degree.)