http://armsandthelaw.com/archives/2013/11/wellregulated_1.php I'm late to the party and half of everyone else who gunblogs has had their 2 cents at this, but here's mine which covers it in a marginally different way.
Turns out if you look back at writing of the time of the 2nd amendment, of which there's plenty since they didn't have email, "well regulated" meant "it works".
This is actually still the case, much as people who are in favor of banning everything will attempt mental gymnastics to deny. They will instead say that "well regulated" means "controlled by the government".
A regulator valve is placed onto a device to control something within it, typically found on air tools to give adjustment from extreme high pressures. The purpose of this regulator? Make the thing work.
Companies have internal regulations. These regulations are made within the company, to set up the method by which the company works. Their purpose is (supposed to be) to make the company work effectively.
I've heard that a properly aligned set of gun sights are said to be well regulated. The meaning? They work.
Heck, even government regulations are technically just supposed to make things work better, and would actually do so if they were only applied to proper places they were needed (which is to say, places where there there would otherwise be absolutely nobody who would/could make people play nice together, and would have problems with the Tragedy of the Commons). In practice, this isn't the case because government rules spread like a plague, but if they were actually interested in making things work effectively instead of trying to take control of everything because MORE POWER, it might work that way.
Basically, the point is that no matter how vehemently people deny it and seem convinced that only asking for government control of everything everywhere, well regulated just means it works. If the "well regulated militia" can, without government control, be told to gear up and go deal with an invading army/aliens/zombies/etc, and does so, then they're sufficiently well regulated.