I’m definitely an Evernote fan, but that’s also because it suits my mobile approach to things very well with its iOS apps and requires a minimum of fuss on the desktop version to do things like OCR documents.
I store just about everything in Evernote, from bills and statements to recipes, and use it extensively for project notes. I link those projects notes back into OmniFocus where they’re directly connected to a task or deliverable, and handle my note-taking and brainstorming almost entirely in there.
Alternatives that I’ve tried include many of the ones listed here, although I’ve generally been satisfied with Evernote enough over the years that I’m not really sure what more recent versions now provide. Devonthink Pro Office was the only one that ever came close to Evernote for me, but the big downside, as I mentioned earlier, was the lack of robust iOS support.
I also looked at Microsoft OneNote recently, just out of curiosity. Despite being a Microsoft product, they’ve done a pretty respectable job of it, and if you were looking for something a bit more freeform in its note-taking and layout approach and could live with a more limited feature set (OCR was particularly odd, although I believe the latest Mac version improves that), it doesn’t look like a bad solution. However, it’s pretty basic compared to what Evernote offers.
Others I’ve looked at over the years include Yojimbo, Simplenote, Notational Velocity, VoodooPad, Notability, and a few others whose names I can’t recall off the top of my head right now. Simpleton and Notational Velocity were actually really nice, clean, frictionless solutions if all you wanted was basic note-taking capabilities, and in the early days, I used Simplenote alongside Evernote, since Evernote’s early iOS clients were anything but frictionless for taking quick notes. Fortunately, Evernote has improved in leaps and bounds since then, and while one could argue that solutions like Simplenote are still more straightforward, it makes little sense to keep notes in more than one place now that Evernote can do the job reasonably well.