2 things in particular
Refactor
When you see code that murkys up the waters of your IDE, refactor it so it makes sense so it's easy to read.
Comment
Use refactoring to compartmentalize 'how' but use your commenting to show why.
Just like Steve McConnell says in Code Complete 2, follow the Psuedocode Programming Process (in this case, after the code is written). It will help you and any future developers read the code.
