I've been wondering for a while what exactly this gem does and I haven't been able to find any definitive answers.
For context, during the final quest for the Mages Guild, Hannibal Traven kills himself and fills this gem with his soul in the process. He says that, "With this gem in your possession, you will be impervious to his attempts to enthrall you." Of course, it is entirely possible to head off to Echo Cave and confront Mannimarco without taking that gem. Presumably, something bad happens if you don't.
However, I can't find any evidence that this soul gem has any effect whatsoever on the quest. I opened the Construction Set and looked around. The soul gem itself (MG17MiscBlackSoulGemFilled) is just a miscellaneous item without any script attached. So it would only have an effect if something in the game checks if the player has it during the confrontation. I then opened the "Use Info" report for MG17MiscBlackSoulGemFilled and it reported that it is only used by two other references in the game:
- The TestQAClutter container: A copy of this soul gem is inside this chest. The chest is only found in one of the testing cells and so is irrelevant.
- The HannibalTravenScript: This script is attached to Hannibal Traven. The only thing related to this soul gem the script does is add a copy of it to Traven's inventory just before he kills himself.
Finally, I tried looking at Mannimarco himself to see if there is something there that would be affected by the gem. I found that when you approach him, he is scripted to cast the spell MG18MannimarcoImmobilize at you. If it hits, the spell disables the player's controls and Mannimarco starts talking to you. Once he is done talking, he then casts his Enthrall spell (MG18MannimarcoEnthrall) at you. The thing is that all the Enthrall spell does is re-enable the player's controls and triggers Mannimarco to fight you. There is absolutely nothing in that spell's script which takes the soul gem into account. I don't see anything on the Staff of Worms which would be affected by that gem if Mannimarco happens to try use it during the fight. None of the other spells he has are affected either; they are just ordinary spells that other NPCs can also have.
So as far as I'm concerned, there is no point whatsoever in grabbing that soul gem before you leave as it has no effect on the game at all. If anyone else has any insight or knows anything that I missed, please do say something.
On a side note, I also found and was amused by the fact that the Immobilize and Enthrall spells are both marked as hostile and don't have the "Disallow Spell Absorb/Reflect" checkbox ticked. This means that any amount of Spell Absorption, Reflect Spell or Resistance to Magicka has a chance of making those spells not work. The latest Unofficial Oblivion Patch also doesn't fix these oversights.