I've collected a couple of my posts on WiX techniques and turned them into a reference white-paper for your convenience.
At the moment, this paper contains just two sections:
NAnt and Wix Versioning discusses one way that versioning can be injected into a WiX installation from a NAnt built script.
Upgradable MSI Installations with WiX reviews the necessary elements for installations that cleanly upgrade.
Update 30/10: New version of the whitepaper that includes a key step previously missing (definition of the Custom action "PreventUpgrading").