I'm in the one uber-database school of thought. On the surface, DevonThink a sort of half baked finder replacement, and if you use a lot of databases, it becomes less baked. The brilliance is in it's ability to find connections between your material that you might not be able to find ordinarily. If you're going to split up databases, the ideal way to do this is via spheres of life, so if in addition to being a religious studies doctoral student, you also do some technology journalism or computer science research and don't see these projects/resouces ever possibly overlapping, then separate databases are fine, but if there *might* be connections, or it's part of a specific sphere or project: keep it all together.

Basically no matter how you swing it, it's going to be huge after a few years of grad school, and it's all about managing that huge-ostity. I think the key in terms of organization is just dump all the files into a big folder and make liberal use of the "replicant" and comments features (for project planning) and just trust the program's ability to help you find things later.