First of all, let me apologize for not posting in several days. Unfortunately, this situation will continue as my time is quite limited because of university stuff...
Anyway, to the point of this post. A few days ago I found an interesting article that talks about free software and good user interfaces; you can read it here. It starts giving a summary of what a good UI should be, why free software can design good interfaces (comparing UI design to code design) and whether commercial companies help or hurt this process.
Later on, it describes the "too many preferences" problem. It explains why a bloat of costumization options leads to an unusable program, and what can be done to improve this situation. I wholeheartedly agree with the author's comments after having used GNOME 2.x for a while. Specially, Epiphany and Imendio Gossip are two excellent applications in the usability field. They Just Work (TM) and don't lack any important functionality.
An example of why too many customization makes programs difficult to use can be found in this analysis. It is a bit old (applies to GNOME 1.4), but is still worth reading.
So, if you are a developer, and your programs have a graphical interface, consider making their UI usable (and accessible). Read the GNOME Human Interface Guidelines for more information, and ask the UI experts (through the existent mailing lists) when in doubt.