I know that I have been just dealing with microbubbles with my top-of-tank scrubber (temporary), but I think I have come up with a better way of doing it versus the couple that SM has sketched up. I tried the long perforated partially submerged pipe, and that did not work at all. I did not try to flat box with the bottom outlet, or the double-U pipe, but with the amount of flow I'm using it just isn't feasible - the small bubbles blow right through since there's nothing to impede the flow.

So up until now, I have been using a couple of pop bottles jury-rigged in place to at least divert the flow of bubbles, like this



and it was doing OK until I rearranged the tank and it wouldn't stay in place anymore. So I came up with this, you can see it in this video at about 5m 30s. If you don't jump to that point, you will get a nice tour of this tank that has only been running a scrubber since October 2010 and has only had about 4 15-20% PWCs, 2 of which came after moving the entire setup twice in one week.

http://www.youtube.com/watch?v=LrNvqtk7t18

I removed the lower 2L bottle, then cut a slit in the 1L bottle and inserted a section of the plastic canvas. My inital idea was to use that to create a break point by which the falling water would not impact the top of the tank water. It helped a little, but large bubbles were still making it through. Then I realized that this made a nice little seat for some bio-balls, of which I have about 3 gallons worth, so I finally put those to use. Now the water hits the balls, and makes only a slight trickling sound (watch other videos of this tank and the scrubber noise is completely overpowering), and the bubbles coming out of the 1L bottle are significantly less than they have ever been.

The bio-balls have the perfect ability to slow down water flow and provide points for bubbles to conglomerate. The downside I could see of using them is that I will have to clean them now and again, and if there's ever a large detachment, it's a pretty nice clog point, so having a safety overflow buit into it would probably be needed for true safety. It's not perfect (i.e. there are still bubbles) but this is just the first iteration.

My scrubber microbubbles are probably much more prevalent than anyone else's I've seen pictures of, because of the vertical drop of the water out of the scrubber. My guess is that a similar bubble diffuser would work for just about anyone with a microbubble issue. Mine probably needs a longer extension down into the tank or a wider outlet, and another layer of bio-balls before it does a truly excellent job of removing bubbles. But, this is only a temporary setup anyways, and it's not my tank - contents transferred from a customer's tank that was about to burst a seam.

And it's worth throwing in there that microbubbles are not proven to do any harm. They're just annoying.

http://reefkeeping.com/issues/2004-01/eb/index.php