At the time of writing (January 2010) the complete Programmer’s Reference Manual(PRMs) is not available on-line. Although, the goal is to document the full workings of RISC OS 5 on-line, this will take some time.
The RISC OS 3 PRMs in PDF form is freely available here.
Any feedback about this manual is most welcome. The preferred method is by use of the General Forums. You are required to register an account at this website (free to do so) before you are able to post.