Hello.
I recently installed Inkscape 0.91+devel, and I would like to make a suggestion.
In version 0.48 often I had a problems with too many unused gradient in the list. At 0.91 you have created the opposite problem. In the new version if there is no object that uses the gradient, and hence there is no gradient.

I propose to add a button next to each gradient in the list, clicking on which you will lock this gradient. In this case, even if all the objects are removed, the gradient will be in the list and it can be applied to a new object.