As for kill all or bosses: it depends how much it slows you down. When I kill Memphy, I kill Memphy, pop the chest at the back and leave. With the Ancient Tunnels I killed everything and I'd say most of my good drops were from normal stuff.
Speed > MF. Everytime.
Oh and ATMA the Single Player Muling Utility (see Stickied Thread in SPF) has a drop calculator which is very useful.