I usually have a lot of windows open within indesign eg pages character styles etc. And I tend to move these around and minimize them frequently depending on what I am doing.
This means I often take longer to find a window than I could if they were color coded and not just text and an icon.
Is there any plug-in that anyone is aware of that will do this, or make windows more distinguishable in any other way?
Unfortunately there's no way to color code them. What I can suggest is that you take advantage of Workspaces in InDesign. I'm a big fan of docking panels instead of floating them to keep them organized and then saving them as a workspace. I have several saved workspaces for the various types of work that I do. For example I have one that I use when doing interactive documents like Fixed-Layout EPUB and a totally different one that I use for working on print collateral and the like. I think you'll find that it really helps you to find the panels when and where you need them.
Most panels (or all panels rather) have a keyboard shortcut.
I can never find a panel by looking or going through the menu system.
Instead, I learned all the keyboard shortcuts for the tools I use, and it's far quicker for me to use a keyboard shortcut than remember where things are put.
You can even create your own keyboard shortcut sets. https://www.google.ie/search?q=indesign+custom+keyboard+shortcuts&ie=utf-8&oe=utf-8&client =firefox-b-ab&gws_rd=cr&ei=_D3…
Or - use Quick Apply to call up a panel or other command http://www.tech4pub.com/2012/09/12/indesign-cs5-5-tip-save-time-with-quick-apply/