MaxP's kit is stunning quality, and it have a couple of their pouches and many of their bags. The ones I use tend to contain all sorts of smaller items including, pens, a torch, paracord, prybar, mirror, knives, whistle, nail clippers, ink cartridges, lock pick, etc. etc. etc. most of the things can help get me out of a fix.
When it comes to loading my panniers, although one of the above pouches would work loaded differently, I have taken to using small heavy gauge self seal plastic bags for organisation do the smaller items: small tools, spare nut and bolts, tyre levers and puncture repair materials, and even coffee whitener. These allow things to be filed away nicely, be ready when needed, be protected by the toughness of the plastic and kept clean and dry. They also take up little space. If I lose one then I haven't lost everything.
