I think the stoory goes something like this:
In the 1990s the JAA was a 'club' of European Aviation Authorities [signatories to the Cyprus Arrangements] who agreed that they would make their national regulations compatible. To this end they agreed common codes for (amongst others) Commercial Air Transportation (CAT) in Aeroplanes - JAR-OPS 1 and CAT in Helicopters - JAR-OPS 3.
When the European Union arrived on the scene, for political and legal reasons, it took over responsibility for all aviation regulation in the EU (and, through EASA, by bilateral agreement in other associate European states too).
The JAA ceased to exist on 30 June 2009 [i.e. Cyprus Arrangements dissolved]. Consequently, JAR-OPS 3 is an orphan code.
EU-OPS (which is actually an annex to the EC regulation [No 216/2008] setting out the Essential Requirements for aviation regulation) is a temporary measure dealing only with CAT for aeroplanes. The rest of aviation operational regulation is currently in accordance with national regulations – although these may originally have been based on JAR-OPS.
The EC regulations for the detailed conduct of aviation operations (the Implementing Rules – ‘IRs’) will deal with all operational aspects of aviation. These are in process of being developed under NPA 2009-2 and have now reached the stage involving review of the Comment Response Document (CRD). When the IRs are published as a regulation in 2012, EU-OPS will be redundant.
When studying the forthcoming EU regulations applicable to helicopters in NPA 2009-2 (see EASA website), good references would be ICAO Annex 6 Part III Section 2 and JAR-OPS 3 where CAT (helicopters) is concerned and ICAO Annex 6 Part III Section 3 for General Aviation (helicopters).
You will see that NPA 2009-2 contains many of the provisions originally contained in JAR-OPS 3 (including those contained in the HEMS Appendix). It should also be compatible with ICAO Annex 6.
Hope this helps