I've customised Reaper with my own varitations of the default theme which I didn't like too much.
I've also set all my Melda plugins to the same colour as my Reaper theme to create consistency.
In Reason, I sometimes added custom backgrounds to my Combinators too.

(Right click on the combinator background and choose 'Select Image'.)
I think it is always a bonus to be able to customise software gui's. It can help with accessibility, not just for visually impared people, but for people who love a programs functions but find the stock gui revolting (which happens a lot)....
I love the way Adobe Audition allows users to drag each element of the interface to whatever size or position is useful. This means you always get the layout you want, not just what the devs want.
Fruity Loops allows for custom themes to be loaded too.
More customisability please devs.