I have made very good experience with Koo Light Manager. Suprisingly the app (I’ve tried the free version) makes the FP2 notification LED shine not just red but also blue, cyan, somekind of orange and others - without the Fairphone update, we are still waiting for, and without any superuser stuff, but simply by running this app.
With the full LED range working now (after the FP2 update to 1.2.8) I can recommend “LED Blinker Pro”. The paid version (2,84 €) not only lets you set LED colour and flashing mode for any app you want (not only a given selection like in “Koo Light Manager”, if I see it correctly) - but also gives you control over individual vibration strength and notification sounds. I was searching for an app that can do the latter for a while - and now I find it in this LED app as a pleasant surprise. Seems to be well worth the money.
But what about showing a notification while LED shows battery loading? Does a Missed Call notification overwrite the Battery Loading notification?
In fact this was the case with Koo Light Manager - until the Fairphone 2 Update 1.2.8. Now the Battery Loading notification light dominates the other(s). 
Yes, I just checked it and unfortunately it’s the same with “LED Blinker Pro”. The app doesn’t overwrite the phone’s standard settings in case of the charging light. Even if I set the charging notification to a different color and flashing in the app (so it could take turns with the other notifications) it stays slightly yellow and turned on constantly.
Does anybody have a clear orange LED notification?
My “orange” is more green/yellow-ish. It’s a little bit confusing when u start charging ur phone and the LED shows a nearly green light even though ur battery has like 10 % left…
Has here anybody a solution for my question about changed notification-LED behaviour after Update to 1.2.8 in this other post?
https://forum.fairphone.com/t/fairphone-2-os-version-1-2-8-6-april-2016/16328/75?u=therob&source_topic_id=11636
Can anyone tell me if there is an option to disable the notification led in FP2? I know that there’s supposed to be this option in settings -> notifications and I can even find the point with the search bar but I don’t seem to be able to actually access it?!