I'm noticing a "clunk" or "thunk" sound whenever the right pedal reaches about 1:00 when I'm standing. I've heard it during seated efforts as well that were closer to mashing (i.e., dying up a hill). Normally I don't hear a thing though (just sitting and cruising along). It seems to do it in most (all?) gears -- definitely both rings in the front and a couple cogs in the rear.

The cassette has about 2,100 miles on it. I replaced the first chain when the Park Tool chain indicator was showing 50%; the second chain (a Wippermann -- the connector link still looks fine) is currently showing 25% wear. It's running an FSA ISIS bottom bracket, which has the same 2,100 miles.

The crank arms don't seem loose from just trying to wiggle them by hand. Any other ideas as to what to check or what this could be? How would I narrow down where this is coming from? I figure that it's always occurring when a pedal is at about 1:00 must mean something.

Crankarms, chainrings, pedals. We just went through this 2 weeks ago. Search the forum.

Pedal bearings, improperly torqued crank arms or bad bottom bracket bearings, thats about all it can really be.