Peter Jacobs at CNCmasters just wrote a step by step guide to calibrating your CNC:
Step 0: Collect All the Tools
Step 1: Level the Base
Step 2: Square the Bridge (X-Y Alignment)
Step 3: Square the Front-to-Back Backbone (Z-Y Alignment)
Step 4: Square the Side-to-Side Backbone (Z-X Alignment)
Step 5: Alignment of the 4th and 5th Axis
Simple step by step guide and some final thoughts.