The suggestion for making the settings window resizable prompted me to post another wish I've had: searchable settings. BBEdit, which has a PhpED-like long list of preference panes, gained this a while back after Apple added a similar feature to the system preferences. And, as a 14-year daily user, I'm amazed at how often I use it.
If you supply a good search index, this would probably cut down on the "can I control xxx feature" posts here in the forums just because people have forgotten about (assuming everyone's read the docs!) or couldn't find a particular setting.
To see more about BBEdit's implementation, go here:
http://www.macworld.com/2006/12/reviews/bbedit85/index.php
It's discussed briefly in the text, and there's a screen shot of it in action.