No matter how small film and video equipment gets, it is still like packing for a third person. Microphones are the worst, because they need to be well-protected, but they come in odd sizes. This usually consists of two shotgun microphones, a wireless microphone kit, as well as two lav mics, a blimp, and lots of odd parts and accessories. Recently I posted about this to a forum with lots of documentary filmmakers, and they suggested the following options. I'm still thinking about what might work best, but here is the list:

• Someone pointed me to this recent Cool Tools post about Op/Tech wraps. 
• Might work well with the cloth tool bag or bicycle courier bag. 
• Or maybe in a mailing tube like these. Or, fancier ones, like these.
• The Pelican 1080 hard case has adjustable interior padding and is what most people recommended.
• And someone else suggested cigar tubes, or boxes.