Fishing in a farm pond (3acres) recently that is pretty crowded with blue gill and stunted bass, I noticed something I've never seen before: about one in three blue gill had small red bubblely looking scores on them, some in several places. Anybody have any idea what these were? I kept out all the ones I caught like that. None of the bass that I caught had them.

Hard to be certain, but could be a couple of things. Overpopulation weakens their resistance making them susceptible to all kinds of stuff - parasites, diseases, etc.... Usually I see the sores on fish post-spawn. This stresses their sytem pretty good. Bluegills should have come of the nest not too long ago, so it might be that. If the sores are still there in October, might want to consider culling. Might be worth a call to your extension agent or the VDGIF biologist. They should be able to offer some good advice on how to improve the health and quality of the fish.