*sigh* Ok. Remember season 1? When Suzaku was arrested for Clovis' death? Well Lelouch/Zero came up with a plan to save him, which was to Geass Jeremiah. When Zero drove up to the execution parade Zero said out loud the word "ORANGE' right before he used his geass on Jeremiah. Zero said the word as a codeword to make it look like it was all a set up to let him and Suzaku go when they were attacked. Afterwards Lelouch/Zero said the word orange had no special meaning, he could have said banana or apple and it would have had the same affect. It was just to mess with Jeremiah and cover-up the geass with making it look like him nand Jeremiah were working together.
Then he got the nickname 'Orange-kun' after that because of that "codeword" and everyone thinking he was a traitor and stripped him of his status in the army. It's to make fun of him and degrade him.