I've tried a whole bunch of different apps for storing reference material (Yojimbo, DevonThink, Notebook, etc.) and have recently settled on
Together 2.0 (I have no relationship with the company that makes it). It's $40 and Leopard only.
For one thing, it's a very Mac-looking app that's a pleasure to use. But the killer feature for me is the ability to preview the contents of all file types that are supported by QuickLook in Leopard so I can quickly see what's in my files without opening the app: txt, pdf, MS Office, iWork, Mail.app's .eml files, web archives, etc.
Even better, there have been recent updates to some of my key apps to support QuickLook: OmniGraffle, OmniPlan, and MindManager.
Sure, I could use the Finder to browse in QuickLook/CoverFlow, but I find Together's iTunes-like interface to be much better for previewing.
It also stores all your documents in a Finder folder structure, not in a giant proprietary database like Yojimbo.
A downside is that it's not quite as snappy and sturdy feeling as DevonThink and Yojimbo. I'm not sure how it'll scale up to really large libraries.