I had this exact problem about 6-7 months ago. The bike only clicked when I was pedaling, didn't matter what gear I was in, just click-click-click 80x/min on every ride. I ignored it for a week or two because I had been meaning to get a tune-up anyway, but then I did a 60-mile charity ride where the click was driving me batty by mile 30. I gave in and checked with the mechanic at one of the rest stops. After eliminating everything else on the bike (not even sure he heard the clicking while it was on the stand--I couldn't hear it from where I was standing), he did think it was the bottom bracket. Since there was not much he could do in the field, I just rode the rest of the route and took it to my LBS the next day for a tune-up and asked them to clean and re-pack the bottom bracket also (the field guy's advice).
They did that, I took it home, and it was still clicking. Through some trial and error, I figured out that when I unclipped one foot, the click was either much quieter or went away completely. Also, it didn't click at all when I rode in the rain. That made me think it was the pedals (SPDs) or the cleats, and it probably wasn't the cleats because I tried with two different pairs of shoes. This went on for another few days until I scheduled another service appointment. On that one, they figured out that it was indeed the pedals that were causing the click. I replaced them, and the problem went away.
So, yeah, it may well be the bottom bracket, but it wouldn't be a bad idea to check your pedals too.