VCK is a common program that has been banned by Battle.net. Furthermore, Blizzard has stated that it will be watching the use of programs that allow multiple logins (listchecker comes instantly to mind). There are some sophisticated tools out there to allow LAN games to be listed on B.net servers to allow for better gameplay and additional features like changing the game name, auto refreshing slots, tracking leavers and jerks, and allow for the formation of a private game (so that your buddies can join) and then turn it into a public game for others to join in.
In other words, third party programs have fixed most of your issues and you know what the interesting part of it really is? They often use the LAN feature of Warcraft III. No LAN feature, no control. I have a feeling that there are more reasons beyond piracy issues that are causing Blizzard to take its position on this.
Anyone else have ideas?