My home-town compatriot Jeremy Thake has hit onto a governance topic that I think will turn into a very popular series once he is done with it (in committing to writing it, he will be a busy boy indeed for a while I suspect 🙂 ).
He has written a post on current methods and common issues of deployment of SharePoint customisations from dev to staging to prod, with particular reference to the current pain associated with iterative development and deployment.
The state of play in this area out in SharePoint land is not the best, due to a wide variety of factors and Jeremy sums it up very well.
Certainly, there are some extremely annoying architectural quirks. Back when I did the branding series I encountered some, but Jeremy has hit some nastier ones than what I found.
Anyway, take a look at his post – its a good read.