I like the Harlequin idea. One of our players had a whole army of those acro-bastards back in the day (1990 or thereabouts). His brother now has an Eldar army. Once of Prince Yriel's pirates (sneaky fella by the name of Cael) helped transport the group to their current location, so he's probably manuvering his own group to intercept them at the Eventus Noctem (or will, once he figures out what the PCs are on about).
The other suggestions are great. I, too, am somewhat reticent to include too many table-top elements (CSM especially). But perhaps one Aspirant Chaos Lord (call him Iago, I suppose) leading a group of hereteks, mutants and others in his own search for the Talisman. He'd love to present it to his own Lord Abbadon, wouldn't he?
So... the areas of the 'Noctem nearest the docks are civilized (mostly). Here we have low end scum and some mutants. Deeper in, beasties and Iago and his band of malcontents. Deeper still, a Space Crusade dungeon crawl from the old days! At some point Cael and his boyz (and girlz) show up, along with Iolanthe Rathbone's Acolytes led by the vile Eisengrimm. This will clench it for the PCs that someone within their master's organization is leaking info to Rathbone. They'll have something to do when they get home.
This brings me to the involvement of Cael and company. They know that their master is known to use the decadent Eldar Xeno-scum from time to time. (Rhynn is known as The Grey Hand among the Calixis Sector's Eldar population, the PCs themselves have been referred to as the Fingers of the Grey Hand) The two times that Cael has appeared, he's been an ally. This time, however, he'll want to prevent the group from accessing the Talisman. It could get tense.
As for the Dark Eldar, we played PtU. The DE leader got away in the last fight. It would be good continuity to bring him back for more fun in the depths of the Eventus Noctem.
Other NPCs include:
Acturus Rhynn - The party's Inquisitor
Dione - Sororita, Rhynn's Prime Acolyte, the person he trusts above all others. She reminds him of his daughter who was killed so many years ago.
Marcellus Ong - A cyborg trapped in a vat of green life-sustaining fluid. He hates his life, and is plotting the overthrow of Rhynn and his Acolytes. Served alongside Rhynn's master and his master's masters for centuries. Still serves Rosenberg.
Hieronymous Rosenberg - Excommunicate Traitoris Heretic Inquisitor, pulling Iolanthe's strings, wants the Talisman for himself.
Wolfe - Hive Scum, friend of the party's Scum - Captured by Rathbone, he's been transformed into a malconid and will be hunting the group when they return to Sibellus. (Malconids are wall-crawling, razor-clawed, mind-wiped killers. Rathbone has uncovered the secret to creating them, and is not above using the party's buddies as weapons)
Constantine Escher - Diminutive Necromundan Genius, loyal follower of Rhynn.
Those Acolytes from Purge the Unclean - the remaining few members will be in on the hunt for the Talisman along side Eisengrimm.
It occurs to me that I don't run games, I run high-tech, low-life soap operas.