The biggest pain with muddy rides is having to clean your bike after. Here are the simple steps I go through after a muddy ride to keep it running like a champ.
1. Spray and Hose - Avoid getting water in these areas
2. Dry Off - After you towel it down, take a minute to dry yourself off and let you bike air dry some more
3. Lubricate - Avoid rust, but also avoid over-lubing