I am a huge Scrivener fan. I usually make a Scrivener project for every subject or project that needs a lot of disparate pieces of info pulled together— notes, PDFs, images, web pages, etc. It is also the best tool for writing because of the ease of rearranging chunks of info. The Mac version allows you to drag web pages in as well, html intact. Also, there is an iOS app for it. The company that makes Scrivener has another little app called Scapple which is a nice complement to Scrivener, as it allows you to create diagrams and flow charts on a free form page to help think through ideas and connections, then import the pieces to Scrivener.
I adore OneNote as well, and use it mainly as a big flexible whiteboard for handwritten notes, collages of notes, sketches and projects as I am working on them, PDFs and Word docs, web pages, etc. it will do OCR on your handwriting just like Evernote. It feels very much like a notebook that you can write or paste things on anywhere. But I do not use it for long writing projects that require a lot of editing. Always Scrivener for that.
I have also relied on Evernote for years as a place to keep thousands of bits of info of every type for easy retrieval. Syncs among all devices and has best in class OCR and search features. It is not a writing tool really. And as it is one giant database, you have to use notebooks inside it to separate your notes into specific projects. You can also add custom tags to notes. I consider it a dumping ground of things that I may need later. It is one of the apps I rely on most in my business.
Devonthink is a highly rated Mac-specific app that is in the same category as Evernote as a tool for organizing and retrieving info, but I find it a little complex and I don’t Iike that it is not cross platform.