Since he already knew I was ready, I decided to walk away from the trigger rather than to ask him to stop clicking his pen. He made a comment about my walking away, but I just calmly (not angrily) replied that the noise of the pen clicking was bothering me and I didn't want to interrupt his conversation. That he should just come down to my desk whenever he was ready. He came down about 5-10 minutes later and we had our discussion without any further comment about what happened upstairs.
After lunch, we had a team meeting conference call with our outside consultants. I came a bit late (they changed the room at the last minute) and sat down next to my coworker from this morning, so that the table was balanced with two people on each side. About ten minutes into the conference call, he started popping off and on the pen cap again, but this time I had to stay where I was. I tried putting in my earplugs but I could still hear the snapping of the cap over and over. Since he was actively leading the meeting, I knew there was no way for me to quietly ask him to stop, so I started writing a note to ask the question. I realized that I didn't phrase what I wrote well, so I began to turn the page to try to write it out again. Before I could do it though, he looks at me and puts his closed pen on top of my notebook. Somehow, he realized that the noise was distracting me again. I smiled and put the pushbutton top pen I was using on his notebook in the open position so he'd have something with which to write, but in the back of my mind I hoped he wouldn't start clicking that too. (Luckily, he didn't. He used a sharpie he brought instead.)
When the meeting was over, I asked if he saw the note I started to write, and he said yes, he had caught a glimpse of it; however, he said at the same time he also realized he was snapping his pen as he was doing it. He was very understanding about the whole thing. I really believe that because I asked him so nicely in the morning, instead of being angry about it, he was very respectful and considerate of my sensitivity. It all goes back to my comment about how the message is delivered when communicating any discomfort to someone else.