Alex Payne's recent post The case against everything buckets makes a strong point in favor of using the filesystem for filing. To paraphrase: If your problem is that you have a bunch of files you need to search through, and possibly tag, then the filesystem and Spotlight are probably closer to solving your problem than you expect.
I enjoyed reading his post, because I like rules of thumb for simple design, and one of my favorites is "why not just use files?" - there are often reasons to do something else, but the filesystem is faster, more reliable, and more open than anything you're likely to come up with on the first try. So you'd better be sure you're not just poorly reimplementing it.
Buzz Andersen has a thorough response, centering on the fact that VoodooPad is a very useful app. Certainly I agree - I use it all the time, and its hyperlinking sets it apart from other notes apps (and the filesystem). So yes, VoodooPad is a Good Idea.
But is VoodooPad really an "Everything Bucket"? I'm not sold - you can use it to store PDFs and images and other files, but it really focuses on pages, and those files are just attachments to your pages. I see it as a notes app. I think if your problem is keeping notes - with images if necessary, linking between them, and searching those notes, then VoodooPad is clearly better than the filesystem. But you don't have to put everything else in there too.
I agree with Alex that I don't want one program to keep everything in a proprietary database. I like apps that keep my files as files. (like EagleFiler.) But I do want layers on top of the filesystem - you wouldn't want to use just files for email, for example.
The only solution that's always bad is the solution to someone else's problem.
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