I, and I think a number of others, have turned to LightFlow for our LED color controlling needs. I conversed with the developer about some features I'd like to see added to LightFlow, and it turns out the features are not included because they are either hardware specific or require code that is not included in Android's source code.
The first would be to use ICS's (this has been in ROMs for a while) swipe-to-remove-notification feature to tell LightFlow that the notification has been cleared. Ice Cream Sandwich, at this time, provides no information on the event to other applications. It's even been added to Google Code as a requested add-on.
Issue 23106 - android - Have a way for accessibility service to detect when single notifications are cleared in Android 4.x - Android - An Open Handset Alliance Project - Google Project Hosting
The other thing I asked for was more synchronized cycling of the colors between different notifications. The rate that colors of the LED changes on a GNex is independent of the rate one chooses to flash the LED... The result for me personally is that I will see the same notification color flash twice, and then cycle to the next color... or in mid-flash, the color will change.
My question to the ROM developers is if one or both of these can be implemented without waiting for Google - thus providing the functionality to LightFlow to operate correctly. Of course, the developer of that app would then have to add something to their own code, and I have no idea if they would do that, but perhaps if the functionality were available in the ROM, we could be convincing?