What is the best culinary practice surrounding the water used to soak beans, pulses and rice?

That water may contain all sorts of fungicides, dust, contaminants, rodent feces, insects, and so on. The process of production of beans is far from sterile. If you wash the beans thoroughly before soaking, you may avoid it, but a common kitchen practice is to just dump dry beans into water, maybe rinse once to get rid of the worst of the possible contaminants, then soak, stir a bit to detach whatever might have been stuck, and drain, and you have nice clean and well hydrated beans.

The other reason to discard the soaking water is (theoretically) limiting flatulence.

According to The Bean Institute and other sources:

Soaking overnight and then discarding the soaking water leaches out sugars in beans that are responsible for gas production.

Scientific evidence supporting this is weak and contradictory. However, it hasn't been disproven, and many cooks and nutritionists believe that a long soak followed by discarding the water reduces bean-generated flatulence. For this reason, the common practice is to soak for 8-12 hours, discard the water, and rinse off the beans.

Maybe the women in your family would shocked because they had the practice of soaking beans in bicarbonate of soda. That is going to give up some unpleasant taste if you cook them in that liquid. Lentils typically need no soaking and you can cook them right out of the pack.

The problem with beans and lentils is that you cannot add salt or any acid during the cooking process. All the flavorings have to be added at the very end after the beans / lentils are thoroughly cooked. If you don't do that you get hard and cooked beans, which goes down about as easy as eating car tyres.

I have found beans and lentils to be a neutral tasting vegetable protein. It is the sauce and the spices that you make with it that makes it tremendous, I never really thought it had much of its own taste. The soaking of beans is a way to break down the fibers of the beans to aids in digestion. Beans are naturally high in fiber something which is painfully lacking in many western diets.

When preparing lupin, the water used to soak them in should be discarded, and even this should be done several times, or it has a bitter taste.

Wikipedia page states that if not prepared correctly, lupin can be toxic.

(This is answer is community wiki so knowledgeable people can improve it. :-) )

The soaking water does not make a difference in the case of beans. Soaking is osmosis between beans and the soaking liquid, nothing comes out of the beans themselves, that is if they don't contain pesticides or other chemicals. The liquid is generally thrown just because it is sitting in open for hours and may contain dirt or impurities.

However, while soaking rice, you should really wash the rice thoroughly first (until the water runs clean) to get rid of the starch and discard the water if soaking is required.

hmmm. I honestly thought this was crazy talk when I read it.
But I give these guys a pretty high reliability estimate:

https://www.fda.gov/food/metals-and-your-food/what-you-can-do-limit-exposure- arsenic

Now that I think about it, Utah, where I live, has some places with a pretty high arsenic content in the soil. Of course, we don't have enough water to grow rice.

Is there ever a case when one should dispose of the soaking liquid rather than use it as additional flavoring to a stock

YES! YES! YES!

Extract from FDA PUBLICATION May 13, 2014 Arsenic in Rice and Rice Products Risk Assessment Report (Revised March 2016) | 2

We knew that arsenic was present in a variety of foods in the U.S. diet but until recently there were not enough data to determine the amount that is inorganic versus organic. To provide information for our estimates of dietary intake of arsenic from rice and rice products, we measured the arsenic levels in these foods. We found that average concentrations of inorganic arsenic – the more toxic form of arsenic – were as follows:

• 92 parts per billion (ppb) in white rice

• 154 ppb in brown rice

• 104 ppb in infants’ dry white-rice cereal

• 119 ppb in infants’ dry brown-rice cereal

Sorry for getting so excited but......Well I am absolutely amazed by both "The question" and "The answers."

Obviously, our health advisors are missing their target with "Stack Overflow" users.

Soak your rice overnight – this opens up the grain and allows the arsenic to escape. Drain the rice and rinse thoroughly with fresh water.

How to Cook Rice to Remove the Most Arsenic

I think this article says it all really, and rice being the main offender does not mean we can just exclude beans & pulses. Personally, I find the statement on organic rice "Whether rice is grown organically or conventionally does not have an impact on arsenic levels" particularly interesting.