What would be the proper way to address such a company in a formal letter?
ms consultants (www.msconsultants.com) and truenorth (www.truenorth.org) seem to be very thorough about spelling out their names in a very particular way on their websites. truenorth even italicizes and bolds half of their name.
So would there be a correct way to designate these companies in the inside address or beginning a sentence?
For the inside address I would keep it lowercase. As the first word of a sentence, I would capitalize it. I wouldn’t pay attention to honoring italics and bolding, although it seems that in truenorth’s literature, they always keep it lowercase and they both italicize and bold it. It’s all a question of style–there’s no real one “correct” way to do it.
(Oh, and i hate that plaintext-bold-no spaces typesetting (or other variation, like italic-bold-no spaces) of brand names. It looks cliched and lazy design to me.)
But WWW address formats encourage companies to run the name together.
StraightDope would be nice. 
The proper way to address such companies is with insufferable pretension. For example, you should right-justify all your text, and you should choose one letter to capitalize no matter where it appearS or how dumb it lookS. Besides, “truenorth” is just a cheezy midwest convenience store chain. Who are they fooling with the .org domain? Why do they deserve a formal letter? I mean, sorry to be so unhelpful, but if somebody asked you how to make Barney like them, wouldn’t your instinct be to ask them why?
How is it registered? That’s how I’d capitalize it. eBay, for example.