Just a one-liner post really. With Magento 1.4.1.0, there is now a setting to disable a category from appearing in the frontend navigation bar. For each category in admin, you will see an option at the bottom of the general information tab: "Include in Navigation Menu".
Add Magento Categories Without Them Appearing in Frontend Navigation
About Tom: Magento Loving Managing Director at Meanbee. Main tasks include coding magento themes, drinking tea and reminding Nick what he should be doing.