He mostly wears his old NIS sweatshirt. Naval Investigative Services. In the episode after Gibbs gets blown up on the ship and his old boss comes back after getting called by Jenny Gibbs and Old boss (forgot his name) discuss the name change.
Gibbs wears a variety of shirts when working on his boat(s). I would say the most frequent ones are the old NIS shirts which was the precursor to NCIS. The name was changed not too long after Gibbs became an agent, but after Franks retired. Additionally, Gibbs wears shirts that are sent to him by law enforcement agencies throughout the country.
NIS (Naval Investigative Servics) are the letters I think you are talking about but Gibbs wears a lot of different shirts while working on his boat. I heard one time that they are all shirts sent in by fans to Mark Harmon.
