A TITAN facility is a great way to be Lovecraftian with your players. TITANs don't need to build things for human-sized or human-shaped morphs, and aren't operating off human logic, so the "facility" need not conform to any human architectural framework. From the visible outside, you can borrow from "[url=http://www.dagonbytes.com/thelibrary/lovecraft/mountainsofmaddness.htm]At the Mountains of Madness[/url]":

H.P. Lovecraft wrote:

The effect was that of a Cyclopean city of no architecture known to man or to human imagination, with vast aggregations of night-black masonry embodying monstrous perversions of geometrical laws. There were truncated cones, sometimes terraced or fluted, surmounted by tall cylindrical shafts here and there bulbously enlarged and often capped with tiers of thinnish scalloped disks; and strange beetling, table-like constructions suggesting piles of multitudinous rectangular slabs or circular plates or five-pointed stars with each one overlapping the one beneath. There were composite cones and pyramids either alone or surmounting cylinders or cubes or flatter truncated cones and pyramids, and occasional needle-like spires in curious clusters of five. All of these febrile structures seemed knit together by tubular bridges crossing from one to the other at various dizzy heights, and the implied scale of the whole was terrifying and oppressive in its sheer gigantism.

Once inside, there are a couple things that I'd suggest:

1. Fractal interior architecture: Everything curves. Nothing meets at a T-joint or right angle, junctions follow upon junctions, and rooms duplicate themselves at different parts of the facility. Once players are well and truly in the structure, make them realize that they might not actually be able to get back out, at least not by remembering landmarks.
2. Mutating architecture: the interior of the building actually changes shape. The players should be able to see this movement, but it should be used to unnerve and/or inconvenience them.
3. A lot of nothing: there should be lots of areas where something clearly had been worked on or an area where something should be kept in storage, but whatever was there isn't. As in, there's a good chance it's wandering around the structure for players to run into at the worst possible time. EXAMPLE: You enter an ovoid room where the walls, ceiling, and floor are covered with cryogenic storage pods like those used to store morphs prior to the Fall. In the center of the room is some robotic surgical(?) apparatus with a number of still-moving manipulator arms. In between these arms is a constantly-changing holographic projection; each new projection shows a transhuman twisted into something monstrous, and every time the projection changes, the manipulators appear to move to begin the process of forming that new monster had there been an unfortunate being within their grasp. Staring at the device in the center only momentarily distracts you from the fact that many of the pods in the floor are open, with pools of condensation in the bottom indicating that something had been stored in there and then revived.
4. The Not-A-Basilisk-Hack: As you design your facility, try just before every time the players find something off-putting that they hear a signature noise. Have it faint at first, then get stronger. It doesn't have to come from a particular direction; in fact, depending on how the players deal with everything else, they may never find out what the noise is, but it should haunt them.

I'm having a lot of trouble narrowing it down without knowing that the dungeon's theme is :) Therefore, a grab bag! :D 1: When your player first arrive, build the fact that the entrance corridor is strewn with cobwebs into the description, don't give it any apparent importance. It's up to your players to realize that there shouldn't be any spiders there to create them :D If they touch or brush up against them, they make the delightful discovery that they're monofilament meshes, and have to make a fray at half to not get their parts chunked. 2. The sound of dripping accompanies the group as they approach a doorway leading into a large room. The walls, floor and ceiling are covered with Terran foliage such as ferns and tropical flower (which is all completely normal and harmless)... and in the centre of the room a huge sphere of water floats in the air. Ripples gently disturb it's surface as droplets "fall" into it from every surface, including the floor. The way forward lies on the opposite side of the room. Synthmorphs can cross the room and interact with the contents with no trouble, but biomorphs who cross the boundary into the room experience agony commensurate with an agonizer as their bodily fluids are forcibly sucked through their skin into the sphere. Willpower tests are needed to enter the room, and freerunning is necessary to get through without taking too much damage. 3. Near the beginning of the dungeon, the team comes to a hexagonal room with two exits. When they approach one of the doors, the other begins to slide shut; if they back off it opens again, and of they approach both then both doors shut... the team must choose an exit. Once through, the other door seals shut. Later, somewhere in the dungeon, they round a corner and are confronted with... themselves. Identical morphs, identical personalities. Discussion or memory comparison reveals that their experiences before and within the dungeon are identical, with one exception... in the hexagonal room, they took the other exit. The exact nature of the duplication I leave to you, though the two teams should probably try to kill each other at some point to avoid to many complications. On their way out have the team pass back through the hexagonal room, but have the doors be closed until they approach. In the room, they find themselves. Dead. Damage to the walls and doors indicates that they were sealed in. For extra Mindscrew, have them have died of old age or starvation; the biomorphs are dried out husks, and the nuclear batteries on the synthmorphs have run out. 4. This is perhaps more suited to a climax, but what the hey: The team comes to a vast cavern, whose walls are adorned with twisted, impossible sculptures. In the centre of the room a large spherical enclosure of thin glass is partially embedded into the floor, and in the centre of that a man sits on a small wooden chair. He is nondescript, with brown hair and eyes, and is dressed like an office worker. Upon seeing the team, he stands up and walks calmly over to the glass, stopping about a meter short. Then he speaks, in a completely calm and normal voice which for some reason the glass doesn't interfere with at all. He says three words. He will not respond to any questions or challenges, but he will calmly repeat these words. The words are: “Let me out”. If the team decides to leave, he will calmly walk back to his chair and sit down. If they break the glass, he will walk out, look at them, and say “Thank you”. The team then takes 1d10 SV and wakes up outside the dungeon with tracks of dried blood running from their ears, nose and eyes. The dungeon itself is a smoking ruin. Finally, an addendum to Thepedant's “Not-A-Basalisk” - have the noise play after every encounter or set piece the team encounters. Each time after the first, imply that the characters realise there's a meaning to the sound, and each time they come a little bit closer to comprehending it. After the climax, have it play one more time, and the characters realise that the noise is (and always was) a question: “Do You Understand?”.

I just finish the third tradeback of Doom Patrol (Vertigo, Grant Morrison) and it make me think about this post, if you want some realy weird think to put in a Titan's bunker I encourage you to read one of those In the first one, the bad guy live in a Mansion full of butterfly pin alive on the walls. He feeds from despair and agony and he's stuck in "no one alive" dimension. SO : your players enter a room full of rows of butterfly, each stuck on their wall by an optic cable who falls to the ground and mesh with other cables and they disappear into some endless darkness of the bunker's corner