Same here- downloaded (paid app) Light Flow app, now have LED for Handcent, Gmail, missed calls, etc. Happy with it.
I called my bionic from a land line, but hung up before I answered. Almost immediately, I got a notification of a missed call, but no led. I turned off my screen and the led started blinking and blinked until I turned the screen back on. Then it stopped. I think the point is that when the screen is on, you have a notification so you don't need the led. When the screen is off, you can't see a notification, so the led blinks. Until you clear the notification, the led will blink when phone is in sleep mode. This behavior started with Gingerbread.
Same Issue here with Handcent. LED would not illuminate.
May sound stupid, but if you have a sleeve or case on your phone make sure that it isn't covering the LED.
Haha yeah i feel stupid now... just found out yesterday that the LED was being covered by the case.