Acrylic with a lot of gloss medium might work. I also tried a paint pen once. I worked, but it was kinda dark...Highlighter works and didn't come off for the week I had it on there, but it was very light.

The best thing to do for sure results would be to replace the led altogether, but I'm pretty sure that that's something that many people, including myself, don't want to try.

Colored cellophane should also work. It would probably be best to adhere it with removable gluestick glue (works like a post-it note.)