I prefer Gmail's non-standard method of handling email, but it's a very poor fit to legacy IMAP clients.
Recently I realized that email I was deleting in OS X Mail.app (10.6) was being archived in Gmail. This is not what I wanted. I feel like this is a relatively new behavior -- at one time one had to jump through some hoops to map Mail.app's delete button to the Gmail archive behavior.
I've had more success with setting OS X to move deleted messages to the Trash mailbox (no change) AND Store deleted messages on the server (this I changed).