If you’re a PC user…it’s Onfolio:
If you’re a Mac user, an answer appears to be Yojimbo:
I’m just playing with the Yojimbo demo now, but on first glance they seem to be invested in a similar space. These applications recognize that the reality is that your input isn’t that neat and organized. Sometimes you have a file, sometimes you have a link, sometimes you have a PDF or an email message. You have to store that information in some logical system that lets you search and pull out what you need when you need it.
Onfolio is more expensive, but it’s also far more complex. In addition to just collecting information, you can also publish what you’ve stored in a variety of ways and you can add a lot of information about your material in such a way that an academic or researcher would need. Onfolio also gives you the option to store a bookmark as a link or as a complete local copy of the page. This is helpful if you think the page may change later and you have to capture it exactly as it currently appears. Onfolio can run as a stand-alone application and in a sidebar in both Firefox and Internet Explorer.
Yojimbo’s main advantage (besides bringing this kind of cataloging to OS X) is that it’s by the fine folks at Barebones. They make good stuff. But since I’ve already purchased Onfolio I’m not seeing a compelling reason to spend $39 to have a similar basket on OS X. I would love something like this that was cross-platform/server-based so I could store information in a central location (on a LAN, not the Internet), regardless of the computer that originally contained it.