I have two systems--folders and bins.
Folders are for collage materials I've encountered, whether printed digitally, ripped from a magazine, cut from a calendar, etc. I have these folders sorted as follows:
Technical (Drawings, Blueprints, Diagrams, Graphs, etc.)
Coordinating "kit" ephemera is sorted by color after I've used the kit. By kit I mean those found in plastic sleeves in craft stores, usually designed to coordinate with a particular paper line. Since this isn't "real" ephemera from my life, my primary concern is managing my color palette. I've got ROYGBP + Black, White, and Brown bins. In addition to ephemera I also have everything else sorted into these bins. Purple glitter lives right next to purple letter stickers and purple tags in my stacking bins. I do have a separate small parts box from Lowe's that holds metal embellishments sorted by metal, attachers sorted by metal, and flowers/ribbons sorted by color. These live on my desk because I'm reaching for them a lot.
"Real" ephemera--movie tickets, receipts, bits of packaging, etc--it all goes into a single container.
When starting a project, I shop my bins and sort my finds into a project bin. Everything goes--punches I want to use, dies, glitter, ephemera, collage, paints, embellishments, papers, rubber stamps, ink pads, base materials like paper bags and chipboard--everything. When I've finished a project I re-shop remainders into the proper containers.