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
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.