As many Logic users are still carefully modifying their custom GUIs, let us start by posting some individual elements that have been modified.
You know the HUGE SCREAMING BLUE on/off button in the plug-in window? It is possible to get rid of it.
Download one of the following ones and drag it into the Resources folder as explained on the Modification page.
Here’s one with several color options (by Lee Wilson; at the moment non-retina only).
The green/grey (on/off) one:
Download link: pluginwindow_button_bypass.tif.zip
In the case you prefer the shape of the Apple default button, yet dislike the color, try dragging either pair of these into your Resources folder (a simple mod by Jus):
This collection will perhaps expand later on.