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.
In the iOS Dev Center developer navigate to "Certificates, Identifiers & Profiles > iOS Apps > Identifiers > App IDs"
Find the app id you wish to delete, highlight it and select "Settings". At the bottom of the resulting screen there is a "Delete" button.
Previously the only way to do this was to use a Safari & Chrome extension written by Simon Whitaker
app-id-sanity downloads
It gives you an "Active" checkbox next to all your App IDs and allows you to relabel them to alter how they appear in the App ID drop-down when creating new provisioning profiles.
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