This is an excellent post and a very interesting subject. Been thinkin' on bacteria myself lately.
I haven't added any bacteria to my pond yet, though I am considering a concoction of Rid-X and Roebic mixed with some warm mucky water.
What I have noticed is that the neighbors dog comes over for a swim several times a day and usually swims on the north end of my pond. Where the dog swims, I've noticed that the muck and algae that was on the rocks in the pond is now nearly non-existent in this area. I'm not sure if this if from the dog stirring up and adding oxygen to the bottom in this area when it enters and leaves the water or if it's just displaced everything out further into deeper water where I don't notice it. At any rate, the rocks in this area are cleaner than anywhere else in the pond.
That's probably close to raking, which I think the best results can be achieved. I raked a small area several years ago and saw very quick results