
Umbranus |

That's difficult. I don't think it is AoE damage but I could see it working. Depends on the question if you could trample multiple creatures in one turn.
As trample is a full round action and it states you can trample any (as in any one) creature I would say that it falls under the "immune to weapon damage and effects that only target a limited number of creatures".

Claxon |

If the swamrm is immune to weapon damage than no. If not, then yes.
For instance, crab swarms are immune to weapon damage so they would not be effected. Visually, you step on some crabs as you trample over the swarm, but it's such a small number that it doesn't effectively harm the whole of the swarm. Mechanically no effect to the swarm.
However snake swarms invovle larger creatures, and they lack the weapon damage immunity. They would be damaged by the trample attack.

Mechagamera |
Looking at the definition of trample, the trampling creature would have to be one size category larger than the swarm:
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.
I would interpret that to mean a large bull couldn't step on enough crabs from a huge swarm to disrupt the swarm, but an Apatosaurus would disrupt the swarm if it walked over it.
That also makes sense that a bigger swarm (like a stampeding herd of cattle) would be able to disrupt a smaller swarm (a huge swarm of crabs).

Claxon |

The size catgeory is simply to be able to make the overrun attempt. Imagine trying to run over a elephant as a human being. Not going to happen. That is what the size category is about.
If the swarm is made up of fine or diminutive creatures they're so small that the steps of the hoves/feet/whatever of the overrunning creature simply don't damage enough of the creatures to cause any mechanical damage to the swarm. A slam attack is a natural weapon, and though tample is unspecified it is only logical that it is effectively a weapon. Swarms that are immune to weapons should be immune to the damage of trample.

Mechagamera |
The size catgeory is simply to be able to make the overrun attempt. Imagine trying to run over a elephant as a human being. Not going to happen. That is what the size category is about.
If the swarm is made up of fine or diminutive creatures they're so small that the steps of the hoves/feet/whatever of the overrunning creature simply don't damage enough of the creatures to cause any mechanical damage to the swarm. A slam attack is a natural weapon, and though tample is unspecified it is only logical that it is effectively a weapon. Swarms that are immune to weapons should be immune to the damage of trample.
I am not sure that I buy your logic. The point of weapon immunity is that a single weapon strike doesn't impact enough surface area of the swarm to cause meaningful damage, whereas an AOE spell or splashing acid on the swarm does. Let's look at trample in that light. If a gignormous kaiju steps on a huge swarm of crabs, it's foot might be bigger than the crab swarm, and I don't think anyone would argue that the swarm doesn't take damage if the foot is bigger than the swarm. So somewhere between the small striking area of a weapon and a kaiju's foot damage becomes possible. I think trampling by a larger enemy is closer to the kaiju's foot than to a sword blade in terms of area.

Claxon |

A ginormous kaiju's step still isn't an area attack. The rules are set in up in a specific way and have specific functionality. Is it reasonable to rule that if a creature is so large that it's foot takes up the entire space that a swarm would be in that it damages (possibly destroying) the swarm? Sure. But it would still be a house rule.
As this is the rules forum, house rules need not apply. By the rules there is no consideration of how big the creature is for whether it can damage a swarm with a trample. A trample attack is a weapon (a natural weapon) and fine or diminutive swarms are immune to weapon attacks by the rules. If you wish to rule differently fine, but it is a house rule.
Trample is not an AoE attack unless the creature has some special ability that specifies it as such.

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Trample is not an AoE attack unless the creature has some special ability that specifies it as such.
Trample is not a single target attack, it affects all opponents moved over. That is the definition of an AoE; affecting all targets in an area. in this case, the defined area is the path the trampling creature moves.
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.
Emphasis mine.
One target or one million, it makes no difference to a trampling creature. Damage is dealt to all. For rules purposes, I would size size requirements still apply. The trampling creature must still be a larger size category to have a meaningful affect.
A swarm is immune to any spell or effect that targets a specific number of creatures....
Trample does not target a specific number of creatures.

Claxon |

AoE refers to area of effect and is generally used to refer to spells only. Further isn't not a game term.
Immunity to weapon damage is a trait of swarms. Unless trampling isn't a weapon then a fine/diminutive swarm is immune. Reasonably, trampling is done with hooves/feet/whatever and should be natural weapons.
The swarm trait that specifies that it is immune to spells or effects that target a specific number of creatures doesn't need to apply here because the swarm is firstly immune to weapons as a separate ability.

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AoE refers to area of effect and is generally used to refer to spells only. Further isn't not a game term.
Immunity to weapon damage is a trait of swarms. Unless trampling isn't a weapon then a fine/diminutive swarm is immune. Reasonably, trampling is done with hooves/feet/whatever and should be natural weapons.
The swarm trait that specifies that it is immune to spells or effects that target a specific number of creatures doesn't need to apply here because the swarm is firstly immune to weapons as a separate ability.
Read the bolded text I just quoted from swarms; Spell or Effect. Nothing prevents physical attack, as long as the attack is not restricted to a specific number of targets. (Most attacks are.)
Swarms are immune to effects that target a limited number of targets. Trample is not limited.
You argue immunity to weapons. I ask you this, how many weapons deal automatic damage with a reflex save for half? Which weapon am I actually striking with? (Trample does not strike with a weapon, it simply deals damage.) Trample is an effect, without being either a weapon or a spell. It is damage applied to all applicable opponents in the area moved through.

Mechagamera |
A ginormous kaiju's step still isn't an area attack. The rules are set in up in a specific way and have specific functionality. Is it reasonable to rule that if a creature is so large that it's foot takes up the entire space that a swarm would be in that it damages (possibly destroying) the swarm? Sure. But it would still be a house rule.
As this is the rules forum, house rules need not apply. By the rules there is no consideration of how big the creature is for whether it can damage a swarm with a trample. A trample attack is a weapon (a natural weapon) and fine or diminutive swarms are immune to weapon attacks by the rules. If you wish to rule differently fine, but it is a house rule.
Trample is not an AoE attack unless the creature has some special ability that specifies it as such.
If you can post a link to proficiency with trample, how much a Great Trample costs, or whether trample is a two handed weapon or anything else that suggests a weapon property; I will buy your assumption that trample is a weapon. Otherwise, it seems like you are just house ruling trample as weapon, and, as you say, house rules need not apply.