I'd say upgrade anything you think you will keep through the entire tier first. So if you have any BiS items, those first. If you're a normal mode raider and probably won't go very deep into heroics, if at all, do the normal mode BiS items that don't drop off any boss you could see yourself killing on heroic. It'll take 24 weeks or so to upgrade everything fully, so wasting a week on something you will replace in a month is foolish to me. That said, if you don't care how long you keep the item you're upgrading, weapons will be the biggest benefit with I believe trinkets being a most likely second.