Hmmm...mutation...mutation...mutation...
Ok, first off. If you don't have it, consider picking up at least the PDF version of Chaositech by Malhavoc. Not only would it blend extraordinarily well with the Daelkyr/Abomination kind of stuff that can happen in the dark places of Eberron, but it has mutation templates, and tables of vestigial and mechanically effective mutations. My personal favorites are the Serpent and Dragon grafts - shoulder mounted, flexible, poisonous or fire breathing combat "heads", and the various "hives", like the mini spider swarm spewing arachnid hive that the user releases from under their tongue.
Having immensely enjoyed mutating some of my own players' characters, this would be an excellent resource, I'd think.
On the matter of cloning, perhaps something a bit more bound to your PCs. Eric Boyd did several monster conversion of old FR monsters on his site at:
http://www.ericlboyd.com/dnd/monsters.html
In the first bestiary is the Alias Vessel, based loosely off the old Azure Bonds novels. Perhaps in an interesting vein, these are the permanent "variant" clones Mordain comes up with. While he can regain a certain level of control or program them with tasks based on various glyphs and sigils embedded in their flesh, they are otherwise free-willed. The Guardian Angels find out about them much later on, and may ally with some of them against others which has gone completely bad. Imagine if you will, the Anti-Gareth. Wait, I'm not sure how different that is.
Anyway...the previous posts are appropriately villainous, here's some added spice:
What about tying either the Shifter's forms, or the Druids Aspects to the Lunar cycle, the seasons, or the zodiac of Eberron. Thus, they shift over time. While this obviously involves a heap o' paperwork, it would keep the player on their toes, and give a the opportunity for giving the vict...beneficiary a wide range of powers over a wide series of play sessions to discover.
Look at the characters' skills...if they have something that they have spent points on, but isn't a primary focus, give them a +2 circumstance bonus...when they use their new improvement. This will be a reflex at first, but they should be able to learn to control it over time. For instance:
Better climbing - 4 spider legs extrude from the body and assist
Better spot/listen - the fingernails of the user pop-up revealing mantis-like eyes, or extra tympanic membranes push out along the tendons on their neck
Better Intimidate - bloody bone spurs temporarily grow forth from the user's brow ridge and jaw
Given Gareth's frequent use of Detect Evil/Thought, there really should be something affecting this. Perhaps giving a boost to the DC, but silver-white light flows from his eyes like Smaug in the old Rankin-Bass Hobbit cartoon.
Perhaps give Six a hive of "fleshweavers", small insectile creatures that live in him, but over the course of say, an hour, grows him a full living skin with cartilage to make those necessary bumps and divots on a living being. He detects as a living being, but it only lasts say, an hour & a half (ala Darkman), before it rots away. But otherwise gives him an excellent disguise skill. It can only be used 1/day perhaps, and occasionally rotting odors and lumps of rancid flesh will fall out of him when he walks when it's not used frequently.
As for geasing them, making that the defense of Nameless seems paramount, since the limitations on the spell in terms of duration with open ended commands wouldn't really keep them away. I always liked the old Contracts of Nepthas, myself, but both parties must willingly sign. Shucks.
Perhaps a variant on the Psionic power (whose name escapes me) that implants a death wish in the target. Instead, whenever they approach Mordain or his demense, they receive images of killing themselves or being killed by doppelgangers of themselves in gruesome ways which causes mounting fear penalties to their rolls, perhaps even a queasy feeling that mimics a negative level when in his personal presence. EDIT: This could probably be a custom curse using the Bestow Greater Curse from BoVD.
I think the best thing to be in place when they wake up should be that they are drained, and I don't mean level drained - I mean they have no spells in memory, all their supernatural or spell-like abilities for the day are used, and perhaps hand out no swashbuckler cards for that session. Until after they've had an actual day of rest in game. That, more than anything else, should worry them immensely about going head to head with him when they wake up. He apparently drained their heroism.
That's all I can think of for now...
PS: Oh, and he should have a Liquid Pain Extractor (BoVD), and should have gotten a nice supply off of them during the experimenting, even if he was nice enough to mind wipe them of the experience later. I'm sure it'll come in handy in a plot later.