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Those patches are part of the low-temp reusable surface insulation (LRSI) that covers a lot of the exposed surface of the shuttle. The patches are manufactured to be a standard 8×8 inch patch, with small gap-fillers placed in between each patch (hence the small bumps around all the edges). They do seem to be extremely random in application on the vehicle, but I can only assume that their assortment is based on expansion of the material to ensure that any displacement is spread evenly throughout the surface. There is a good graphic showing the different materials used [here](http://en.wikipedia.org/wiki/Space_Shuttle_thermal_protection_system#mediaviewer/File:ShuttleTPS2-colored.png).
edit: It seems that my memory was not entirely correct (been a while since Materials class) and the LRSI tiles were replaced with “Flexible Insulation Blankets” on Discovery. They seem to serve the same purpose and just weigh a little less, so my initial theory on the “random” placing of the patches still seems valid.