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I've investigated DevonThink, Yojimbo, and EagleFiler. DevonThink is clearly the power tool of this bunch, but I just can't get past the unapproachable user interface. I really like Yojimbo, but it can't handle email natively; you have to print emails to pdf to import them to Yojimbo. EagleFiler feels sticky some how; it's lightning quick one minute, then impossibly slow the next. But it takes a mountain of email, a huge variety of other documents, and provides all the hierarchical and tagging-based organization I could want.

So EagleFiler gets my email, web clippings, random notes, and anything else that doesn't have a home elsewhere.
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Cheers,

Curt