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I think Evernote will accept gmail urls if you want to have everything in one place. I also quite like Curio from Zengobi for arranging larger project materials; and Scrivener for largely writing related projects.
There are quite a few programs that will hold reference material. It all depends on what you want to do with it really. Scrivener as i said is good for writing, Curio mostly for freeform brainstorming, evernote for everything that needs to sync and be mobile, Journler for most other scraps and pieces.
That's only my personal collection of course. There are Yojimbo, Tinderbox, Personal Brain, MacJournal, etc etc.