Trample states: Trample (Ex) As a full-round action, a creature with the trample ability can attempt to overrun any creature that is at least one size category smaller than itself. This works just like the overrun combat maneuver, but the trampling creature does not need to make a check, it merely has to move over opponents in its path. Targets of a trample take an amount of damage equal to the trampling creature's slam damage + 1-1/2 times its Str modifier. Targets of a trample can make an attack of opportunity, but at a –4 penalty. If targets forgo an attack of opportunity, they can attempt to avoid the trampling creature and receive a Reflex save to take half damage. The save DC against a creature's trample attack is 10 + 1/2 creature's HD + creature's Str modifier (the exact DC is given in the creature's descriptive text). A trampling creature can only deal trampling damage to each target once per round, no matter how many times its movement takes it over a target creature.
Overrun states: As a standard action, taken during your move or as part of a charge, you can attempt to overrun your target, moving through its square. You can only overrun an opponent who is no more than one size category larger than you. If you do not have the Improved Overrun feat, or a similar ability, initiating an overrun provokes an attack of opportunity from the target of your maneuver. If your overrun attempt fails, you stop in the space directly in front of the opponent, or the nearest open space in front of the creature if there are other creatures occupying that space.
When you attempt to overrun a target, it can choose to avoid you, allowing you to pass through its square without requiring an attack. If your target does not avoid you, make a combat maneuver check as normal. If your maneuver is successful, you move through the target's space. If your attack exceeds your opponent's CMD by 5 or more, you move through the target's space and the target is knocked prone. If the target has more than two legs, add +2 to the DC of the combat maneuver attack roll for each additional leg it has.
Currently what's under contention is whether a creature can simply chose to avoid another creature's Trample or a Stampede of several creatures due to inheriting rules text from Overrun, making the ability to make a reflex save for half damage redundant and pointless.
