There are numerous companies that offer software for HAZOP's, PHA's, etc. I was involved in large PSM projects a few years back and, while I'm not familiar enough with the different software offerings available to recommend one over the other, using a software product helped the facilitator with the organization of the study, provided consistency in the process, and produced convenient reports for dealing with recommendations and for record-keeping purposes.
From what I've read, the organization of the study includes the leader or facilitator, a recorder, who actually runs the software, and the members of the design or review team.