(asked yesterday over e-mail by Nilina Mason-Campbell, and answered so quickly because it's easy for once)
Picture book manuscripts should be paper-clipped. Novels should come loose-leaf, as hopefully I'll want to copy it to share it with other people; but if the manuscript arrives in a box or a folder, it stands a good chance of being read more quickly, as 1) it will stand out on my manuscript rack and 2) because it's more easily transportable, I can grab it on my way out of the office to read on the subway or at home. (It will also likely be returned to you in better condition if it comes in a box or folder -- I'm physically hard on manuscripts, I'm afraid.)
Picture book manuscripts should be paper-clipped. Novels should come loose-leaf, as hopefully I'll want to copy it to share it with other people; but if the manuscript arrives in a box or a folder, it stands a good chance of being read more quickly, as 1) it will stand out on my manuscript rack and 2) because it's more easily transportable, I can grab it on my way out of the office to read on the subway or at home. (It will also likely be returned to you in better condition if it comes in a box or folder -- I'm physically hard on manuscripts, I'm afraid.)