My latest post was based on the research I did a few months ago when I decided I wanted to learn how to build wheels. I read the information on Sheldon Brown's site (linked to above), a lot of other articles and forum discussions and a wheelbuilding book. It was also based on my training and past experiences. Prior to this thread, I had not once given a second of thought to whether or not bicycle wheels were balanced or not. Other than the blurb I remembered reading about the valve stem hole always being across from the seam/weld.
I have ridden in cars with unbalanced wheels and have heard about various types of machinery self-destructing due to improper balancing. However, I think these cases are due to much higher RPMs and much larger imbalances than are likely to be found in a bicycle wheel.
I have no doubt that most bicycle wheels are not balanced - because they don't need to be. I think it would be really difficult to make a bike wheel unbalanced enough for anyone to notice. People add/remove things like reflectors, computer magnets, spoke cards, etc. all the time with no noticeable (at least that I have ever heard of or experienced) effect on ride quality.
There are too many other variables that affect ride quality much more than the balance of a wheel. Legs moving up and down, whole bike and body swaying back and forth, bumps in the pavement, springiness of the frame and tires, etc.
You say that you can feel a difference in ride quality after filing down the weld beads. How much weight do you estimate that you removed? Depending on the alloy used in the rim/weld, I guesstimate it would take about a chunk about the size of a valve cap to weigh one gram. That's a lot of metal to remove, so I'm assuming you shaved off only a fraction of a gram from each rim. If each wheel with tube & tire weighs a pound, the entire bike weighs 20 pounds & the rider adds another 150 pounds, the effects of balancing the rims seem to become negligible.
I suspect that the improvement in ride quality you claim to feel is all in your head. It makes sense that after all the time and effort you put in to taking your wheels apart, observing how they spin, shaving the welds, etc. that you want to feel an improvement. However, without more data and experiments to back it up, I have to (no disrespect intended) call BS.