The Doctor likes very much of all types of experiments and modifications. You don't have to even ask for most exotic things.
Modification: Switch in teeth to provide eletric shocks to himself. Pressing the switch for 1 second provides slight shock, 3 seconds knocks him unconsious. Any longer than that is not recommended.
Acquired how: Personally requested.
Modification 1: Berserk button system.
Acquired how: Direct result of being mindraped in Mission 2. Didn't have much of option.
Experiment: "Mindrape" resistance testing. The test included of being subjected to mentioned "Mindrape" and observing its effects on her brain. Eventually the experiment tested a system to prevent mindrape by resetting her brain. It seemed effective.
Acquired how: Faith stated that she needs something to prevent "Mindrape".
Modification 2: Medical mutant. Left arm produces fleshy bandages. Right palm has orifice that ejects organically produced medi-foam. Capable of feeling what is wrong with body by touching. Elongated teeth to inject painkillers and coagulant boosters.
Acquired how: She asked if it's possible to create small living organism to produce medi-foam.
Modification 1: Albino mutant sex-change operation gone a bit wrong. "May have gotten carried away". Resulted Inhuman Visage effect (+1 speech for intimidating, -1 for anything else).
Acquired how: Elizas asked to be turned into an attractive female after being mutilated by The Armory Master.
Modification 2: Feminization. The doctor got carried away again. The point was to become a bit more feminine, but end result is a fertility goddess.
Acquired how: Asked for it.
Modification: Long tentacle arms, six legs capable of climbing on the walls. He got proper ones after complaining and designing his own version.
Acquired how: Asked for alternative limb cybernetics.
Modification: Full-body robotization. Only part of his brain left, superfluous parts removed. Lasers on right hand fingers for cutting things. Left hand works as electric shocker. Left palm has rocket slug launcher. Right arm contains Gauss shotgun. 360° vision with cameras on head. Protectorate level armoring. Overdrive controls on chest (bonus for strength and dexterity rolls). Long cleaver with scabbard on back. Skin of his human body's face made into a creepy mask stretched over his robot face.
Acquired how: "Can you upgrade me?".
Modification: 3 meter tall robotic giant. Metal skull with cameras on eye-sockets. Gauss Gatling gun in right arm, cutting laser in left. Both can be used with arms attached. Barrel in palm. Permanent tesla arc in mouth. Activates when jaw is opened. Laser drones. 20 of them. Mild intelligence. Charged Particle cannon in chest. Long charge, very powerful. "Make sure to dig in before firing". Bullseye mode, computer aids in everything, built directly into brain. Never miss a shot. Only good for one shot though as it has long reset. Body is very strong and very durable, but is slow. Custom weapons consist of a short, shotgun looking thing (Gauss Shotgun, like an overly large gauss rifle, but with a shortened barrel, different type of grip and trigger and a clip full of large blackshot gauss rounds), a longer rifle with a large clip (Gauss Assault Rifle, resembles a huge gauss rifle as well, but with a larger square clip full of redshot gauss rounds, expanded barrel and what look like parallel generators) and a very long, very heavy looking rifle with a scope on it (Particle Condenser Sniper Rifle, it doesn't seem to have a clip of any kind, but isn't a laser either. There's a rather large generator built into the stock and 4 soda can sized capacitors sticking out of one side).
Acquired how: "Hi, I was wondering whether you can turn me into something useful. More specifically, if possible I would like you to turn me into a killing machine. As long as I can keep my personality that is."
Modification: Genetherapy to increase reflexes. Side effects include extremely low pain tolerance, even slightest pain will cause every nerve scream in pain. All pain killers are toxic to him, except one (only The Doc knows which one).
Acquired how: "Id also like to know if there is a gene therapy or something similar that could make my nervous system more powerful?" with additional threats towards The Doctor.
Modification: The human spaceship, farting through space. And bony armour. And he had three legs for a while.
Acquired how: "Would it be possible to... enhance a biological organisim to be able to survive is space, without a suit?"
Modification: Head replaced with metal head with a bear trap jaw. Has since regained an organic head.
Acquired how: ?
Modification: extremely flexible robot body with limbs like Doc Oc.
Acquired how: ?
Modification: Regeneration, permanently locked stats, turned into a mindless training dummy.
Acquired how: Asked to be made strong.
Modification: Extremely fast and agile custom robobody. It looks skeletal thin, has several extra joints, and is covered in ceramic armour. Kinetic amps in hands, feet, elbows, and knees. His brain is modified to keep up with his body. The Doctor also gave Renen an an extremely sharp blade (true mono-atomic blade) that must be unsheathed and used immediately before it brakes. It reforms when re-sheathed.
Acquired how: Impressed the Doctor in a sword fight. Became the Doctor's apprentice.
Modification: Black scaled Zeus-fish with ability of electric eel. Has webbed fingers and gills on his neck.
Acquired how: Asked the doctor to make him better. And complained a lot.
Modification: Shapeshifting ability. Capable of absorbing biomass and use it to fuel transformations.
Acquired how: Specially requested for it.
Modification: A catgirl. Literal one, to point she can't even talk anymore.
Now a cyborg catgirl, with chameleon fur and medical fangs
Acquired how: Genemodding paid for by teammates.
Modification: He has 6 arms now. Two really big muscly ones, those ones have the bone pistons, and then 4 more normal ones. The normal ones are longer, designed for use with other weapons, ones that don't need as much strength. He has some good organic armor plating on the primary shoulders and arms, as well as chest, back, head and neck.
Acquired how: ?
Modification: Had their bodies (and physical stats) swapped.
Acquired how: ?