I think Edit menu > Find/Replace can probably help you a lot. It can be configured to select all kinds of specific objects or styles or attributes (or other things). You can even use XML to select. There's probably only one tutorial for that, which is still a fairly new feature (it's not entirely intuitive) and the manual hasn't been updated in a while. Locate the article on Inkscape in this issue of Full Circle Magazine:
http://fullcirclemagazine.org/issue-122/ And there's the much simpler way, which is Edit menu > Select Same.
Also there are some less known selection techniques which might help. For example, touch select.
http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Select.htmlI'm not quite sure what you mean about defining a shape-color. The colors are just colors, and I don't know any way to make a particular color only work on certain types of objects (if that's what you mean). It is possible to create a custom palette - one way is a new palette that would be available for any file, and the other way is a per-document palette.
Hopefully the better selection methods will help, but if you still are looking for a shape-color, if you can explain it a little more, we might know some way to do it.
Edit
Oh, the "shape-color" thing just hit me. What about clones? Change the color of (or anything about) the parent, and all the clones change at once!
http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Clones.html