UPDATE: Beta version of online service now available here.
A series of pages have appeared on the Governments official gov.uk website suggesting that the Home Office will be launching a new online application process for EEA nationals on 1 October 2016:
The European passport return service is available for EEA and Swiss nationals applying online using the EEA(QP) or EEA(PR) application forms.
The service appears to be restricted to those willing to use the official EEA(QP) and EEA(PR) forms in an online format. Included as part of the service is the possibility of securing swift return of the passport used to make the application. It seems the online form is completed first and then accompanying documents submitted afterwards. If certain local authorities are used to submit the documents including the passport, the passport can be returned immediately to the applicant.
The service seems to be available only to EEA nationals, not to family members.
The new service is presumably the same as that reported to have been tested earlier in September. I will post more information as soon as it is available.