I have been playing around with a supercapacitor, 1F rated 5.5V. I charge it mostly through USB, which usually takes a couple of minutes to reach a good amount of energy. I have been thinking about a way to indicate when it is charged, and it doesn´t need to be super accurate. Anything with a transistor and a couple more components would do.
What about something like this? Adjust R1, R2 to taste. The LED turn on curve won't be too quick, but for rough purposes it might be alright. Make sure that you've got a current limiting resistor for your charging capacitor.