Blizzard Entertainment launched a newly redesigned Battle.net webpage and converted any Blizzard Store accounts to Battle.net accounts.
Additionally, World of WarCraft players can merge their Battle.net account and WoW account. This change is basically organizational, but will require you to use your registered email address as your WoW account name at login.
In games like WarCraft III, there are no changes. In fact, you cannot log in with the new Battle.net account. I have tested Diablo II or StarCraft, but I would assume they are the same as WarCraft III in this respect.
Then why should you do this? Beta opt-in! Within the account options on the new Battle.net is a opt-in checkbox for upcoming Blizzard beta tests... you know, StarCraft II and Diablo III. In fact, rumors point to the StarCraft II beta starting up soon so get on over to Battle.net and register. I'll be looking for people to play when the beta starts!
The new account will also let you manage CD-Keys and digital downloads for any Blizzard games that you own. Remember, you can register boxed copies to get a digital copy for PC and Mac!