Methods for finding graduate programs for specific areas of research
Look at affiliations in papers.

When I was looking for a PhD position, I systematically did an extensive literature survey. I didn't really read the articles, looked mostly at the abstracts, but I particularly looked at affiliations. At the time, I simply wrote down all academic institutes I found that were in Europe. In a more extended version, one could somehow assign a score based on the number of papers coming from a certain institution and the impact of each paper.

The big advantage of this is that one will find mostly groups doing active research in the field. Whether we want it or not, published peer-reviewed papers are (at least in my field, atmospheric sciences) the method for determining impact. I won't find groups that fail to publish using this method, but I probably don't want to do my PhD there anyway, so nothing is lost from my perspective.

For my PhD I ended up staying exactly where I already was, but now I'm about to do the same for finding institutes with a post-doc. It's one degree more complicated now because of the two-body problem, but even there: my significant other and I both make such a list, then we'll plot them on a map and look at pairs that are close to each other. But it all starts with:

Look at affiliations in papers.