I like the Univenture sleeves, especially the gatefolds. Bags Unlimited carries them and Guitar Center sells them under their own name.
As for storing them (or the paper or tyvex), I like the "drawer" type CD cabinets. You can multiply the jewel box capacity by at least 4 to figure out what they'll hold. Easy access flipping through the discs, keeps them our of the light and dust, and looks nicer.
I have one that looks like this
http://www.racksandstands.com/prods/Leslie-Dame-Enterprises/CD-150/Browse-by-Style-Drawer-Storage/0C2126/0PLE1035.htmbut it was handmade made by an ebay woodworker, has a tab for labels outside the drawer like a library card file, and cost less.