Something I would find highly useful in the gimp is the ability to group
together several layers in the Layers, Channels & Paths dialog.  So, for
example you can turn several layers on or off at the same time with one
click if they are associated with one another.  I would also like to see
maybe some kind of user selectable color association built into the layers
so you can tell them apart more quickly at a glance.  i.e. user can set the
unhighlighted background of one layer light green when it's not highlighted
and when it's highlighted it turns dark green, etc... This would make it
much easier to work with graphics that are very complicated or have large
numbers of layers.