I tend to keep occasional image clippings from pdf documents, images or internet posts along with certain notes in org files and, at times, it gets really hard to move them around because of the links to some relative directory and all. I am now trying to make these files self contained by putting the bytes inside the org files in a separate block. Here is the package if you want to give it a try. The screencast below shows the system in action:
In some ways this violates the plain-text idea of these files but it's not that bad really. Unless, of course, you start embedding things like fonts, audio clippings etc. 1 and start going fully towards something like odf.
This is missing a few features to make it actually usable. A notable one is support for org exports (at least for html so that I can use them in this website).