Alex Limi has an excellent post on the overuse of checkboxes in Firefox's preferences screen. It reminded me of something Nat mentioned during his talk with Miguel de Icaza back at Linux Bangalore 2003 about Gnome. They mentioned several UI idioms including checkboxes and disabled menu items, but the gist of it was, every time you give the user a decision to make, you're making their lives harder. As the domain expert for this product, it's your job to pick sane defaults and not bother the user with these choices.
We took this to heart on the Ayttm project. At the time ayttm probably had over 200 user modifiable configuration options in the preferences screen, and each plugin could add its own. It was way past the point of violating one of our primary design requirements, that it should be easy enough for Colin's mum to use. We had a bit of a dilemma though. While our target audience was definitely non technical, we had a significant number of geeky early adopters who really wanted the ability to modify everything.
Over the next few days we stripped out almost every configurable option from the Preferences screen, however, we left them all in the config file on disk. Any user that really wanted to modify the options could edit the config file in their favourite text editor and make the changes themselves. This made everyone happier. Our technical users were happy that they didn't have to click through too many screens to change all their options, and our non technical users had a preferences screen where the most they'd have to do was enter their account information, and the type of smileys they wanted.
The Gnome Human Interface Guidelines cover a lot about designing intuitive interfaces, so go read that.