This can easily get into a much-too-long discussion about modality of your information and so on, but here are my sacred rules for information management:
- OmniFocus is my central nervous system for everything related to Projects.
- Evernote is my central nervous system for odds-and-ends and general knowledge.
Those two facts work hand-in-hand with the following corollary:
- Each Project has a Name. This Name, like a child's name, is unique to a project, and must be used in its complete form. This is the tie that binds us; it minimizes "glue" necessary to keep a system together. When a piece of information is tied to a Project, it will have the Name of that Project in some form or fashion. If the information is a random file, it will live inside a folder with the Project's Name. If it is an email, it will live in a folder with the Project's Name. If it's a web bookmark, it will be tagged with the Project's Name. And so on. And so forth.
I use the OmniFocus Project's Notes field as the be-all-end-all of information for that project. That doesn't necessarily mean that EVERYTHING lives inside the OF document, but I know I can ALWAYS go there to START looking for something tied to a project.
Info that is SOLELY tied to A project goes directly in the Project's notes. In my job, a "Project" usually comes with a link to one or more web pages, several files on my hard drive, and some random notes. I'll add links to the web sites directly into the notes section of the project. I'll also include an alias to that project's folder on the hard drive. If a project is big enough to require its own folder/tag in Mail.app, I'll create that, then note it in the Project notes. (Man, I wish you could create hyperlinks to Mail.app folders in addition to specific messages).
Notes are where it gets really tricky. Most of the time, when I start taking notes, I just open TextMate and start typing. After I'm done, I have to decide what to do with it. If it's info that's only applicable to a project, I put it in journal-style in the notes of the project. (Some of my notes sections get pretty long.) If it's more "general info" about technology or something like that, I'll add it as a new note in Evernote and tag it with my Project Name.
If stuff really starts to pile up in a project, I'll create a Smart Folder in the finder that searches for my Project Name (there it is again). This will show me EVERYTHING related to the project. I'll link to that from the OF notes as well.
tl;dr: Separate project-related and general information. If something's tied to a project, make sure it's connected to something that has that project's name in a form you'll use repeatedly.