I store the media in one of the CD binders (the big CaseLogic zippered things that holds 4 discs to the page). I toss the packaging and most of the hardcopy material from both HW & SW since it is of little added value these days - most real info is in softcopy form on the discs. The "manuals" are usually just install instructions or thinly disguised advertising. I have one of those magazine file boxes that holds the paper stuff I keep.
I have a drawer on my desk with all manuals and CDs.
I try to keep it organized, but at least when I've needed something, I'm able to find it there pretty quickly.