Hey, everyone. I've been lurking on these forums for a while now, since way back in 0.31.08 or thereabouts. Now that the new version is out, I've been inspired to do some !!science!! regarding transformations, and I felt compelled to create an account and share what I've found out so far.
[CE_BODY_TRANSFORMATION]First up is the [CE_BODY_TRANSFORMATION] tag itself. I haven't yet tested all the CE_ parameters, but the tests I've done so far show that START:<time> and END:<time> both work correctly, whereas PEAK:<time> does nothing, as far as I can tell. It is also possible to have a start tag and no end tag, to allow permanant transformations.
For example,
[SYNDROME]
[SYN_NAME:wolf transformation]
[SYN_CLASS:WERECURSE]
[CE_BODY_TRANSFORMATION:START:0:END:15]
[CE:CREATURE:WOLF:MALE]
will turn you into a male wolf for 15 time units (TimeUrists?).
[SYNDROME]
[SYN_NAME:delayed wolf transformation]
[SYN_CLASS:WERECURSE]
[CE_BODY_TRANSFORMATION:START:15:END:30]
[CE:CREATURE:WOLF:MALE]
will do nothing for 15 TU, then turn you into a male wolf for 15 TU.
[SYNDROME]
[SYN_NAME:permanant wolf transformation]
[SYN_CLASS:WERECURSE]
[CE_BODY_TRANSFORMATION:START:15]
[CE:CREATURE:WOLF:MALE]
will permanantly transform you into a wolf after a 15 TU delay.
Transformation EffectsThe act of transformation heals all wounds, including otherwise-pemanant nerve damage and scars, and so can be used as an emergency healing ability.
As far as I can tell, transformed creatures are still considered a member of the same entities, which can cause some interesting effects. For example, I modded in a custom werewolf-like creature with [CRAZED] that would turn others into more it with a bite. Bitten NPCs were hostile to both normal NPCs and adventurers. From what I can tell, the NPCs have no problem if they attack former villagers, but if the adventuruer does so, they immediately become hostile. I saw a marketplace full of werewolves and humans fighting, and after the werewolves had been killed, there did not seem to be any humans fighting each other. However, after the bitten humans transformed, I joined in, and the humans turned on me.
If you are a creature with the [CRAZED] tag, however, attacking people does not turn the civ hostile to you. This means that means other villagers transformed into creatures of the same species will be friendly to you, assuming you didn't make enemies with their civ before becoming crazed. It is possible to recruit and/or trade with these creatures as well, if they have the [INTELLIGENT] tag.
One side effect of this is that if you transform into an animal, as long as it doesn't have the [CRAZED] tag (or, I'm assuming, [OPPOSED_TO_LIFE]), people will still consider you friendly, and will even talk to you. Apparently, merchants have no problems with wolves just wandering in their shop and asking to buy something. Good luck carrying coin if you don't have any hands though

Another interesting thing (I'm assuming it's a bug) is that with a delayed permanant transformation, if a creature is affected by the syndrome, the name on their blood changes immediately, even before the transformation takes place. For example, a human with a delayed effect to turn into an elf would have their blood displayed as "<names>'s elf blood", rather than "<name>'s human blood". I haven't tested this with delayed non-permanant transformations, so I'm not sure if it happens with those as well. EDIT: Actually, this was being caused by the creatures I noticed this with having gained historic blood immediately, rather than it being delayed (that is, they have the [CE_BODY_MAT_INTERACTION:MAT_TOKEN:RESERVED_BLOOD:START:0] token). Otherwise, the blood will continue to be called "<name>'s human blood" or whatever until the transformation actually takes place, although any blood they had already shed before the change will still show their new species. If the transformation is temporary, however, their blood retains it's original name. Any blood they shed in the temporary form is just generic "<creature> blood".
Any transformed person becomes a (semi-)historical figure, and is tracked by the game. With the above-mentioned werewolf creatures, people I bit would become werewolves, even if I left the area before they transformed. If they transfomred while I was away, they would be a werewolf when I came back, and would immediately begin attacking people as soon as the site loaded. Hilariously, they would still be considered a part of their original entity, and thus would be dressed in appropriate clothing when the site loaded. This resulted in, among other things, a wolf peasent wearing two pairs of shoes and socks, a tunic, a cape, trousers, and a headdress. Don't ask me how he managed to dress himself
AttributesWhen a creature is first transformed into a new species, their new body's physical attributes are randomly generated, as far as I can tell. These all seem to respect the default attribute range for the new species, since I've had the same adventurer turned into a speed ~975 coyote and a speed ~1800 raven, both about average speed for the species. Any subsequent transformations by that creature into the same shape (it must be both the same species and caste) result in having the exact same physical attributes. This applies to all transformations, including those caused by a completely different interaction.
I had a delayed wolf transformation, which resulted in a wolf with Below Average Strength, High Agility, Low Toughness, and Low Recuperation. Using the same adventurer, i then drank a potion which had an instantanious wolf transformation, which resulted in having the exact same attributes. Furthermore, I belive the description of the creature is also the same every time, although it is difficult to check, since most of the time viewing the description of a transformed creature crashes the game. I did manage check once, and the descriptions were exactly the same, so I doubt it was coincidence though.
This is kept track of even if you have multiple transformations. With the same adventurer, I changed into an eagle, which a different set of attributes. After that, I transformed into a wolf again, which still had the same attributes as the earlier wolf transformation.
Even more interesting is the fact that attribute gains to your default form carry over to your transformed forms as well. Using another adventurer, I became a wolf with average willpower, average spatial sense, and average kinesthetic sense. I then power-leveled him in human form (all attributes were average) by leveling throwing, until he had above average willpower, spatial sense, and kinesthetic sense. When I transformed into a wolf again, the stats were the same, except now those previously-mentioned skills were also considered above average. I haven't tested it, but I also believe attribute gains in animal form carry over to your default form as well.
EDIT: After further testing, I've determined that only physical attributes are changed by transformations. Mental attributes are always the same for the same creature, no matter what form it's in. So far, I've been unable to determine if physical attribute gains in one form apply to all forms, or just the form they're gained in. I've also been unable to determine whether physical attribute gains in animal form carry over to future transformations into that same form, or if your animal form's attributes are always set to the "original" values that were generated when you first transformed. Once I can get my hands on a utility that can display the exact value of a creature's attribute, I'll be able to do more !!science!! on this topic.
MaterialsWhen you transform a creature with standard materials into one with non-standard materials, it works fine while alive, but if you butcher it you get all kinds of weird stuff in its carcass. I made an untamable, genderless plant creature made of highly valuable, unique materials that reproduces by spreading its spores in the drinking water, causing whoever drinks it to turn into one of them, the purpose being to make it possible to create a challenging but profitable sacrifice-and-infection-based 'farm'. Problem is, when I actually butchered the transformed creatures, there would be things like dwarf skin instead of vines, edible dwarf soap in place of eyes, and chopped frozen dwarf blood (!) instead of its heart.
I did some experimenting and found that the butcher materials seem to be based not on what materials are actually part of the creature, but by their position in a list that is defined by the original creature's materials. So if I turn a dwarf (whose first defined material is 'skin') into a plant monster (whose first defined material is 'vines') all of the vines will be turned into skin when you butcher it.
Multiple TransformationsIf a creature is transformed, they cannot be transformed again until the first change wears off. If the transformation is permanant, they are immune to any further transformations. I had an adventurer with a custom interaction that allowed him to turn other people into wolves. After I retired him in a town, I tried to kill him with a different adventurer, but he just transformed me and chopped me to bits when I got close. However, using a different adventuruer, I used a interaction to permanantly transform myself into a werewolf-like creature (Yes, I like wolves. So what?

), and when he tried to transform me, I got the message "<name> gestures! You fall on down on all fours!", but nothing about turning into a wolf.
If you are affected by a transformation while already transformed, the second transformation is queued up behind the first, so when the first wears off, the second one is applied. Transformations count the time when you were first affected by the interaction as when they start, even if they are queued, so the syndrome
[SYNDROME]
[SYN_NAME:queued transformation]
[SYN_CLASS:WERECURSE]
[CE_BODY_TRANSFORMATION:START:0:END:30]
[CE:CREATURE:DOG:MALE]
[CE_BODY_TRANSFORMATION:START:5:END:35]
[CE:CREATURE:CAT:MALE]
would transform you into a dog for 30 TU, and then a cat for 5 TU.
Fortress Mode TransformationsI had dwarves transformed into other creatures, always resulting in TAME PETS
I had dwarves transformed into other dwarf castes, resulting in perfectly normal Dwarves
I had PETS transformed into dwarfs, resulting in TAME dwarves, that otherwise work as usual (skills, labors, equipment) They do have no name though.
Anyway, this is everything that I know so far. Feel free to share your own research on transformations.