Long overdue update: There was a post here explaining how to mess with your iOS settings to get the Mail application to “archive” instead of “delete”, as some people prefer one behavior over the other.
As of iOS 4.2, this tutorial is completely unnecessary, as there’s a setting to choose whether you want the now-default Archive method, or a regular old delete. You can find it in the main account settings for your Gmail account:
I have nuked the previous tutorial, as it was confusing and useless in light of Apple engineering out a better option.