Everything! Anytime the train couples hard, or the slack runs in or out, or they hit a crossing frog a little to fast, the contents will try to shift. In a standard boxcar the solution is to nail the pallets to the floor, and possibly nail dunnage to the interior wood sheathing. That's hard to do with a exterior post steel side, so they started installing various styles of lading anchors. The reason for the waffles was to recess these, so that it was easier to load the car from wall to wall. Otherwise the anchors stick out into the interior, and can interfere with the loads. Unless the car is stenciled for a particular use, you can put anything in it that would go in a similar standard boxcar.
