I bag everything in logical sections (top left, top right, lower left, lower right, etc... more complex machine, more sections) and take pics of those sections, usually in a "semi" disassembled or loose-fit state so you can see where the washers, springs, brackets etc go. Pictures of the final assembled stuff don't do squat for me as most of the 'wtf?' stuff is hidden anyway.

I also will 'reassmble' sub assemblies to keep fasteners and nuts in their respective places if possible (ie put screws and nuts back onto switches or ramps to trap them there)

Personally, I would not group all the screws, washers, widgets, etc... together by type but that's just how my mind works. That's more how I build something from scratch, not how I rebuild something after disassembly.