As a programmer who deals with wordpress on a daily basis I feel like I have a different view to it's inner workings. The simple functions for the_loop(), the_title(), and the_content() are things i rarely touch, as they are more template functions for displaying templates. There is a reply to The post that describes using "do_action" which depending on what you want would be a better option for achieving the formatted post content.
However, I have a real love/hate relationship with wordpress plugins. Writing plugins is very easy, and there is sufficient documentation within wordpress itself to describe most functions. However, there are a LOT of plugins I've come across that are written terribly. I would love to express my dislike of them, however I've taken on the "If you cant write better, then don't criticize" mentality.
Maybe one day I'll feel confident enough in my skills as a coder to name and shame these scripts, but for now I'm concentrating on becoming a better developer, and writing good PHP.