Lightflow works very well for me. I think a lot of the complaints in the play store are because people don't actually read the documentation and understand it's limitations and how it works.
In order to have the LED continue it's indication when the screen is on with a Samsung phone, the phone needs to be rooted, and the root option selected in Lightflow's settings. Even then, this particular function seems a little bit flaky, but when I tested it I found it did work, most of the time.
With an app like Lightflow, or Light Manager, the LED can indicate far more than the few things Samsung uses it for. Lightflow can provide status indications for about 200 different apps. As an example, I have it set to indicate a new Gmail email with a Blue LED, new work email with a purple LED, Calendar events with green, missed call with red, voice mail with flashing white, Words with Friends with orange. Oh, and charging with flashing red and fully charged with flashing green.
And they're prioritized, so a voice mail indicator won't get hidden by a WWF indicator, and work email shows up even if I have gmail, etc.
It's a very slick app. You can control LED colors, flash rates, how long it stays on after an alert, and also configure custom alert tones and vibration patterns for each type of alert. The only real problem I've had is due to a bug in Touchwiz when used with apps that utilize accessibility services. Sometimes these apps, which include Lightflow, will trigger the talkback feature. I had to switch to Nova launcher to solve the problem, but Nova's better than Touchwiz Home anyway, so no loss there.