Thaumaturgist (Rooms F and S) - This evil magic-user's goal is "to take over the dungeon level". Allies include a charmed smuggler (2nd level fighter) and a pet giant snake. Other resources include his tower (home base), a wand of petrification and a captured ape in a cage.
Per Holmes' advice, I've generally had him react to intruders by fleeing and ordering his lackey to attack, but in the Portown Rumors I positioned him as a potential employer in town. Why not have him play the same role if first encountered in the dungeon? He might parlay with the PCs to get them to aid in taking over the dungeon. An easy first mission would be cleaning out the giant rats in nearby Room G. Other targets might be the goblins in Room A, the giant spider in Room J, the giant crab in Room L, the pirates/smugglers in Room M, the ghouls in Room P, or any wandering monsters he's encountered.
Following Zenopus' demise, "[o]ther magic-users have moved into town", which I've taken to mean the thaumaturgist, but it also implies at least one other. Perhaps there is a rival M-U also searching for ancient treasures in the dungeon.
Another option is to have the thaumaturgist as a former apprentice of Zenopus who turned his master to stone and used him as the rotating statue in Room F. In this type of scenario there's the potential for restoring Zenopus with the scroll of stone to flesh. Another twist would be to place on the thaumaturgist on the town council, or perhaps as an advisor to one of the lords on the council.
The only other clue that Holmes gives for goblins' motivations is survival - they will flee or surrender if half the number is killed, and will bargain duplicitously in order to escape. They have knowledge of "the dangerous trap rooms" although it is not clear what this refers to. The ambushing giant spider in nearby Room J is a possibility although it was much weaker in Holmes' original draft (only 1 HD), so I'm not sure if that is what Holmes was referring to.
The goblins' room is very close to the entrance to the dungeon, with no other encounters between, and they could easily slip to the surface to steal food from the town; in Portown Rumors this activity is responsible for one of the rumors.
They have a good deal of coin (1000 SP, 2000 CP), which means they might be working for someone, perhaps the thaumaturgist. If the PCs offer more money, the goblins would probably provide information or cooperation for the time.
One of their chests is trapped with a sleeping gas. In my version I've added that they know how to make this gas and store in it breakable vials, for use as "sleep bombs" (ala the Green Goblin) to help them escape.
Pirates (Room M) - Another group of indeterminate number; there at least four but with a 1 in 4 chance every turn of 2-5 more arriving with no limit indicated. This group is mainly concerned with maintaining their sea cave hideout in the sea cave. They have a dangerous "guard dog" in the form of the hungry octopus they feed as they row in to keep from attacking them. They are also described as smugglers but are probably not currently moving the goods into town through the dungeon due to the various dangerous monsters in the way. But having them use the dungeon for transport could be a motivation for having them vie for control of the dungeon. Alternately, if their lair is threatened they may go seeking revenge on the offending party.
The force in Room M are all described as normal men, but they had at least one former member who was a 2nd level fighter (now charmed by the thaumaturgist). This raises the possibility of stronger leaders that are currently elsewhere. If they feel threatened by the town they might assemble a larger force and stage a raid. In this way the current force in Room M could be used as advance force similar to the bandits watching the Keep in the wilderness in B2.
They have Lemunda the Lovely prisoner. Did they kidnap her with the goal of ransoming her? Or did they catch her spying on them and are now debating what to do?
Ghouls (Room P) - These undead are tied to the cemetery in an ambiguous manner. The room contains some smashed coffins (their own or someone else's?) and the east door "leads to a short dirt tunnel which ends blindly under the cemetery". The coda to the adventure indicates something is going on there: "What inhuman rites are being practiced deep in the ghoul haunted passages beneath the graveyard?" This implies cult activities, which could be another faction. Perhaps the cultists are animating dead bodies - skeletons, zombies, ghouls. The cult would have a leader, possibly an evil curate (5th level Cleric) and many lower level acolytes (Level 1). Perhaps they carry a "sigil" that keeps their undead minions from attacking them. To increase the presence of this faction in the Sample Dungeon, we could add a roving band of cultists to a Wandering Monster table for the level.
Rats (Rooms G, N and RT) - These are not intelligent, but there are many ("there is no end to the rats"). Add a controlling were-rat or two (or even a vampire!) with a base somewhere in the rat tunnels and there's another faction vying for control of the dungeon.
Townsfolk - While the citizens of Portown are not ordinarily encountered in the dungeon, they've got a stake in it since it is under their town and the denizens may pose a threat. Per the coda of the adventure, the townspeople may not take kindly to trouble stirred up from below ("tampering with Things Better Left Alone"). This brings the possibility of invoking the "Angry Villager Rule" - "Anyone who has viewed a horror movie is aware of how dangerous angry villagers are" (see OD&D, Vol 3, page 24).
However, if the PCs gain some prominence - such as by rescuing Lemunda - the town leaders would probably support any efforts to defeat any and all of the above factions. The form of government is not specified, but Lemunda's father (who I've named Leomund) is described as "a powerful lord in the city above". This implies more than one "lord" to the city, and the intro refers to "the authorities", so perhaps there is a ruling council of lords. Gygax's guidance regarding the Castellan in B2 (see page 7) could be useful for role-playing a town leader such as Leomund and his reaction to the party's exploits.