Borrowing ideas from The GIMP, more specifically the IWarp filter. In order to understand what I’m talking about, just fire up The GIMP and play with the filter if you haven’t already 
It has some functionality that would be useful in 3D as well: Restore brush: shift vertices (vertexes, verticies?) towards a goal shape. In IWarp the goal is whatever state the image was in before the filter was launched. However, you could extend the usefulness of this feature by introducing a function to memorize the shape of the mesh (somewhat like shape keys, although I haven’t used them so not sure). You could also think of this as a selective undo feature. Does this make sense? I’ll elaborate if necessary. Swirl: this would work in 3D as well, and if you introduced the 3rd dimension into the mix, even better. Edited to add, apologies for the wall of text, I didn’t know the message editor behaves this way.