If the damage was reduced to 0 by DR (or energy resistance), the additional effects are negated aswell, unless said otherwise on each ability's entry.
The rules for Damage Reduction say:
Whenever damage reduction completely negates the damage from an attack, it also negates most special effects that accompany the attack, such as injury poison, a monk's stunning, and injury-based disease.
A Ghoul's disease is applied on injury (bite attack), and thus would be negated if damage reduction completely negates the damage.
Ghoul Fever: Bite—injury;
However, keep in mind that it does not reduce effects that are energy based or non-physical in nature, so if you have a claw attack that deals an extra 1d6 fire damage, that damage is still applied. On the same line of though, a claw attack that drains energy will also drain energy even if the claw's damage was negated, because the rules for Energy Drain allow them to work even on a touch (no damage), as it says that it simply has to hit the attack.
The Paralizys of a ghoul also does not specify that it's on injury, it simply says:
Some monsters and spells have the supernatural or spell-like ability to paralyze their victims, immobilizing them through magical means.
So, on a rules as written reading, it's safe to assume that even if the damage was negated, a creature would still suffer the paralizing effect, because it's not related to the injury, but a magical effect that afflicts the target. This last part of probably subject to table variation, as many GM's will agree that ghouls are terribly dangerous for their challenge rating.
It's unclear if a ghoul can paralize simply by touching or not, because the paralizys is listed as a Special Attack aswell. You will see the difference when you look at the Green Hag stats, which also has an effect that is applied on her claw attacks, but it clearly states that she must hit with her claws for it to affect the target, or she has to use a special touch attack as standard action to cause the weakness effect.
Damage Reduction does not negate touch attacks, energy damage dealt along with an attack, or energy drains. Nor does it affect poisons or diseases delivered by inhalation, ingestion, or contact.
On this same logic, a disease that simply has a contact as method of transmission would not be negated by Damage Reduction (which is also clear on the rules quoted before).
One of the examples of things negated by Damage Reduction is Stunning Fist, which reads:
Stunning Fist forces a foe damaged by your unarmed attack to make a Fortitude saving throw (DC 10 + 1/2 your character level + your Wis modifier),
in addition to dealing damage normally.
Since you have to deal damage to apply the stun effect, stunning fist does not work if the damage was negated.
Now, the Soul Eater's Wisdom Damage does not say that it must deal damage to work on their target.
Wisdom Damage (Su) A creature hit by a soul eater’s claw must succeed on a DC 17 Fortitude save or take 1d6 points of Wisdom damage. The save DC is Constitution-based.
So it does not matter if the damage was negated, the target will still take Wisdom damage, similarly to how it happens to Energy Drain or contact poisons and diseases.
I would probably agree that all ability damage should qualify as "negate" if it was listed as an example on DR's text. But otherwise i believe that each ability damaging effect should be analized case by case if their effect are on hit or when dealing damage.