Perhaps there is a better way to do this, however one method is to use the System Editor++ to manually delete the application record from the SYSAPPS database table. From the OpenInsight Application Manager select System Editor++, click on the File menu option and select Open Record... Then simply select the SYSAPPS table and open the row associated with the application you wish to remove. Finally click on the file menu and select Delete.
Unfortunately the only way to delete applications is to open them using the Author user. You could reset the users by hacking them in but this requires that you install a fresh copy of OI, recreate the applications using the same usernames, and then copy the user data from new system into your original system. Then you can log in and do the delete. It's a bit messy and not well suited for documenting here as a basic response to a forum post.
Daniel's method might work somewhat, but it won't remove any of the repository items that are keyed to the applications. You really want to do a Delete application to wipe the slate clean.
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Many thanks to all.