I keep textures, meshes, animations and skeletons in different files, my model file is sort of an index of what files constitute a model, so I load and process a model file that in turn loads (or gets references to already loaded) meshes, animations, etc. This way I can mix and match different parts and avoid data redundancy (IE: packing the same texture in two different files).
I removed multiple vertex buffers from my format and instead use a single interleaved buffer, this made sense for my purposes since it simplifies the code and apparently its the recommended way of doing it for mobile platforms (OpenGL ES), that's probably also true for the PC, though a with a quick Google search you'll find out there isn't much difference. Don't get me wrong, Multiple vertex buffer support is good, supporting interleaved as well is better.
Other things I noticed have already been covered.