Actually, they say that if you soak the beans, dump that water, and then cook them in new water, you'll avoid a lot of the...side effects.
They also say that if red kidney beans aren't cooked really well, there's a toxin in them that can make you pretty sick. (I don't actually care for the red beans as much, so I don't cook them on anything like a regular basis.)
So for me, "beans" means either black or white, and if white, usually Great Northern because they're easier to find than cannellinis. (Cannelinis are yummy, though.) One of my ways to try not to generate so much throwaway packaging (not to mention the cost to transport beans in metal cans full of a lot of liquid that's going to be drained away anyway) is to mass-cook dried beans in my crockpot periodically.
I have a big 6-quart cooker, so I can do 4 cups of dried beans at a go. (Not really more than that, though. I think that's about 2 lbs.)
I usually start in an ordinary stockpot, though, just for speed, to get the beans soaked. To do this, put the beans in a big pot, covered with at least 2-3 inches of water. I use my pot with the pasta insert because it makes draining them really easy. Bring it t a boil on the stove and let it boil for a few minutes (some sources say 2 minutes, some say 10, I figure it's a pretty inexact science!), then turn the heat off, cover the pot, and let it sit for at least an hour untouched. (Again, some sources say an hour, others say 5, others say you can leave it up to 24.) Basically, in the soaking process you're just shortening the amount of time actual cooking will take, although some say it also affects how soft your beans can actually get after cooking...My MO is to start the process when I get home from work, boil the beans and then let them sit in their water for a few hours.
Then (usually after the kids have gone to bed) I drain the soaked beans and drop them in the crockpot. At this point, there's a lot more than 4 cups of beans because of all the water they've picked up, so they probably fill the crockpot 2/3 or 3/4 of the way full. Fill it the rest of the way with water (it's honestly at this point about as full as I can get it!) Put it on low overnight, or for 8-10 hours, or sometimes more, depending on how old the beans were and how long you soaked them. The only way to really tell is to test them and see if they taste right.
At that point, I drain them again. At this point I have two choices: either I can put larger quantities in quart ziploc bags in the freezer (they stack very nicely and take up not much space), or if I have more time to futz I put half cup quantities into my muffin tins, and freeze the tins for a day or so. Then I can take the nicely pre-measured "bean muffins" out of the muffin tins and put them back in the freezer in ziplocs, and I have nice, easily thaw-able, pre-measured cooked beans. They are easier to get out of the muffin tins if you plunge the cup parts into hot water for a couple of seconds until the "muffin" loosens. From the original 4 cups of dried beans I ended up with 24 "muffins," i.e. about 12 cups of beans.) I will have to again do the cost-benefit analysis of doing it this way, but in terms of greening my footprint, it's a fairly easy no-brainer.
So now I have a freezerful of black and white beans, waiting for salads and chilies and all that good stuff...