Custom Channels are like folders that let you group individual ad units as you'd like and get performance statistics for the group as a whole.
For example, custom channels will allow you to track how the ads across just your homepage are doing, or determine how well your top-right 300x250 on your 'Sports' section performs.
Custom channels can provide you with the data that you'll need to understand which layouts work the best on your site and which can be improved.