When the work is finished, a final snag needs to be given. However, for large complex work what is the best way to do this ?

I find by far the best way to this is to have a walk thro with the Client , the Client usually writes down any snags, which in fairness are usully cosmetic, i.e Painter work which has been marked or scuffed by other Trades. This answer is based on my experience in doing Renovations, Conversions and extensions.

I agree. Systematically go through the project noting down every snag, minor or more important, which can be given to the builder. If there are any snags that he doesnt think he is responsible for these can be talked about before the work is done. Dont forget certificates for installed services, electrical and other service tests, windows and fire doors.