Alright, here is the updated list:- (The Thyroid gland is the latest addition.)
Adrenal Glands:- replacement changes response to danger - possible gain of rage-like effects (thanks Mayhem!)
Bones or Skeletal Material:- replacement changes resistance to damage and flexibility - possible changes to hit points, possible increases in dexterity or even strength (stronger bones, or more flexible bones, or more pliant joints...)
Brain:- replacement changes personality and memories and mental capacities - possible bonuses to intelligence, wisdom and maybe even charisma
Hair:- replacement changes resistance to cold - possible increase in the ability to endure cold and possible increase in AC (if the fur is particularly thick)
Heart:- replacement changes endurance and ability to withstand punishment - possibly grants a constitution bonus, or a bonus to checks that deal with endurance/exertion, or perhaps grants an increase in hit points, or possibly could grant a haste-like effect (heart rate increasing to enormous levels thus enabling faster action, thought this could also be the property of the adrenal glands)
Kidneys:- replacement changes water retention and resistance to poisons - possible decrease in the need to drink water and possible bonus to second saving throws against poisons (they get flushed out faster)
Liver:- replacement changes reaction to poisons and food storage - possible gain of poison resistance and bonus to saves versus poison, or even immunity against poisons, or the ability to go longer without nutrition, perhaps even ability to go without food altogether
Lungs:- replacement changes breathing - possible increase in the ability to hold breath, or possible gain of the ability to breathe water, or increased endurance
Lymphatic System (Nodes, Vessels, Lymph and Spleen):- replacement affects resistance to diseases and poisons (including drugs) - possible gain of bonus to saving throws or in some cases even immunity to diseases and poisons
Muscles:- replacement changes strength - possible bonus to strength, or poossible increase in hit points
Nerves & Spine:- replacement changes reaction time - possibly could grant an initiative bonus, or a bonus to sense skills (spot and listen), or a bonus to dexterity
Nails:- replacement changes unarmed damage and/or improves ability to climb - possible bonus to climb checks, or bonus to unarmed attack, or bonus to unarmed damage (thanks Terwox!)
Reproductive Organs:- replacements change fertility and ability to conceive, carry a child and give birth - what it says above
Sensory Organs:- replacements change sensitivity of organs - possible gain of the Scent ability, or Low Light Vision, or Dark Vision, or Blindsight, or a bonus to Listen, Spot or Search skills
Skin:- replacements change appearance, camouflage and resistance to damage - possible increase in AC due to natural armour, or possible damage reduction (perhaps only against specific weapon category such as piercing), or possible bonus to hide checks due to camouflage pattern or the ability to change colour and texture
Stomach, Intestines and Other Digestive Organs:- replacement changes food intake and digestion - possible gain of resistance to poisons, or the ability to survive on different types of food depending on source creature, or the ability to survive on less food
Thyroid Gland:- replacement changes ageing and speed - possible slowdown in ageing, or the gain of haste-like capability on self
