I guess as a basic starting point everyone who wanna eat some X knowledge should read "the unix system" by steve bourne, who wrote the first shell (sh). Thats the only book i own about unix and he proved to be quite useful
The truth is you shouldn't really need to use the command prompt for most things. The fact that I see a lot of people heading to the command prompt is either an indication that there are lot of people who want to become power users or that the OS is missing some crucial GUI based tools to do the same thing.
Though since you asked for some pointers I found a few web pages that might help, though because of variations with the Apple version of BSD there will be a few differences: