Reading through this thread I just realise that I have tried tons of those programs. I have registered/bought a few (webgal, weborganizer, qnp), I have made the effort to try to use at least 20 different ones (probably more like 50 if you count organisers, outliners, todo lsts, web based tools etc.), and almost never did I actually end up using them very much.
The key points for me I think is the ease of adding / editing notes - either to grab some notes from a source (web page, email) or to write thoughts down. After that it would be a good way to search and structure, so you don't have to waste too much time organising things in subfolders. Oh, and an easy way to backup, export and share.
To write thoughts down, i seem to use email or open a text editor. I used winorganizer for a while, mostly to help writing documentation, but i don't know why but most times I would still often just open a text file in the text editor and think/write in there.
Looking back the tool(s) i used the most to capture snippets of information have been local website archive, clipcache (i used the demo a lot, was going to register, then the database got corrupted), and the notes tool in opera and previously firefox. Almost all the other tools (outliners, freeform databases, pims) the initial work moving all the information into the sytem and organising it was just too much and I never did it...
In a way it's the same thing with any sort of pim/database - you need to reach a "critical mass" of information put in the system and then it will be more convenient to continue using it than to revert to whatever old system you had. But most tools fail to get me to that critical mass, because they make it too slow to get things in them. As a result you're trying to use them while still needing to rely on your old system... and end up never switching. I think a killer feature would be one that has a "scanning" module which would crawl a bunch of directories you choose, find all the myriad documents in formats it can read (the more the merrier, if possible even word processor or other organiser files), then give you a list where you can tick all the ones you want to import, then import them... That'd get you started in whatever app does that.