Removing App ID from Developer Connection

Update: You can now remove an App ID (as noted by @Guru in the comments).

In the past, this was not possible: I had the same problem, and the folks at Apple replied that they will leave all of the App ID you create associated to your login, to keep track of a sort of history related to your login.

It seems that they finally changed idea about.

App IDs cannot be removed because once allocated they need to stay alive so that another App ID doesn't accidentally collide with a previously existing App ID.

Apple should however support hiding unwanted App IDs (instead of completely deleting them) to reduce clutter.