I keep many reference notebooks in EverNote organized by topic (Computer, Home, Life Tips, Health, etc).
If the material is relatively short and related to a short term project, I'll just put the reference material into the note for that project.
For larger projects with many references, I'll put the notes into a separate notebook for the project.
For other work related references, I tend to use the tagging feature and then put the notes into a couple of general work notebooks.
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