What is the correct phraseology for "runway 03 R”?
Runway 03 R would be pronounced as


  Runway Zero Three Right


As ever, although British, I thoroughly recommend CAP 413 the UK's Radio Telephony manual: 

https://publicapps.caa.co.uk/modalapplication.aspx?catid=1&amp;pagetype=65&amp;appid=11&amp;mode=detail&amp;id=6973

It's mostly ICAO compliant and barring small differences, should contain plenty of information for most operations. You'll see all runways are stated using two digits. Unfortunately I can't find an example of parallel runways in there.



One important note


  Runway Zero Three Right


Designates runway 03R, as opposed to runway 03L.

However,


  Runway Zero Three Righthand


Designates runway 03 and a right hand circuit. Very different things! In real life the chance of confusion is fairly slim, but it's worth noting.




  Is there any standard or preference of one form or the other to reduce confusion during communication?


Absolutely. Considerable effort has gone into the standardisation of air traffic communications in order to decrease the risk of misunderstanding. Page 6 onwards of CAP413 above goes into excruciating detail about how to utilise numbers, for example.