Hmm. A lot of what isn't grousing about the obvious is weak in my opinion, plenty of sarcasm failure.
Avoid including a preferences or options dialog. Instead, let the user use the standard OS provided text editor or an editor of their choosing to edit text configuration files
Yes please. A well-commented plaintext configuration file is a thing of beauty, easier and more complete if your application has non-trivial settings.
Make sure an accidental double-click on a single-click item does something really nasty or unexpected.
Straw aside (deliberately making something "nasty"...), different actions on different click types is a good way of fitting more functionality into a program without adding clutter. Sure, there may be a few WTF moments at first, but expecting programs to be written for clumsy people is overkill.
If you do include documentation, there is no need for printed manuals. Users love staring in to a 17 inch light bulb all day.
Down with dead trees (well, they'd have been cut down already but... ok,. shutting up). Search functions and links can be very useful, whoever wants it on dead trees can print it out (a print-friendly format would be nice).
Begin coding the guts of the program immediately. Designing the UI can come later in the development process.
Sounds like good practice, and not a problem if you make sure your UI is sane and expandable. Would be a shame if you had to twist/withhold functionality to fit into your overblown pretty GUI.
LEGO won't be ready for the average user until it comes pre-assembled, in a single unified look, and glued together so it doesn't come apart.