Our starting point should probably be the fact that there is no standard or normal way of doing things. There are different, equally acceptable ways in which individuals perform the same tasks. Ideally, Bible software should offer a high enough degree of customization, so that most people could feel comfortable using it.Now, customisation is doubtless a great thing - for the relatively small proportion of users who invest enough time to benefit. But to say that standard ways of doing things do not exist is not quite right. For software there are a huge number of conventions that have developed - just think of what you expect to find in the |File| menu... Aside from convention there is no reason why Print| should be here rather than in one called e.g. |View|. (Whose very existence is another convention!)
I prepared the prototype Hypertext Bible Commentary on Amos, (I am currently seeking authors for the online Bible Dictionary that will underlie future "volumes" in the series) and have a collection of photos of Israelite archaeological sites online, other projects include an online audio Bible podcast daily, and 5 minute Bible an audio Bible-blog.