Shapechanging and Transmutation

The business of changing one's own shape or someone else's, or of altering inanimate objects. There is usually a smoke effect attendant on this form of magic. Entries are more or less chronological. I've included the Jekyll/Hyde serum under this heading as well.
  
Shapechanging
Regina shapeshifts into a mouse to get into Rumplestiltkin's prison, and resumes her true form with a dark smoke effect (1.02).

A potion devised by Rumple and administered by Jiminy's parents turns Gepetto's parents into dolls (1.05) The Blue Fairy cannot reverse this (wimp), but she can turn Jiminy into a "cricket" (he's a GRASSHOPPER dammit) and magically extend his life so he can help little Gepetto.

Rumple turns Gaston into a rose. (1.12)

Regina disguises herself as an elderly toy-seller in order to pressure Jefferson into doing her bidding. (1.17)

The Blue Fairy turns Pinocchio into a real boy after he sacrifices himself to save Gepetto from the storm. This is fairy magic, therefore the price concept holds. She later says that she was able to change him because of his sacrifice (2.18). He will remain human only so long as he is "selfless brave and true" (1.20). He fails in that obligation and begins turning back to wood (painfully) when the curse starts to weaken (1.20, 2.18). This effect is invisible to those who do not believe in magic. Without magic, sentient wood is not possible, so he is eventually rendered inanimate until the curse breaks (1.21). Afterward, he flees to the woods in shame and is found there by Snow (2.18). Turns out that he went to the Blue Fairy right away, but she was not able to help him because he failed to uphold the terms of transformation; by dying in an attempt to warn Emma about Tamara he regains his good standing and is turned into a human boy again by the Blue Fairy (2.18). And then into an adult man again by Rumple (4.14).

Maleficent can assume dragon form at will, and has been trapped in that form by the Dark Curse (1.22) and apparently preserved by it (2.20). Dragons can exist in a land without magic, but apparently she can't change back. Her dragon form is huge, winged, has the same horns, and breaths fire. Having been blown up by Emma (1.22), she constitutes herself into a sort of half-serpent form when Hook intrudes (2.20).

Cora assumes Lancelot's form while in the survivors' encampment (2.03), and resumes her own in Emma's old nursery (cloud of smoke).

Rumple turned a butcher into a pig at one point (2.04).

Regina turns Daniel into dust (2.05). That may have simply been a result of lifting the preservation spell that kept his body untouched by time in the decades since his death.

Billy (2.07) identifies himself as having been a mouse named Gus in the Enchanted Forest. Other than a side reference in the pilot ("the animals are abuzz") and the use of bird messengers, sentient animal life does not feature largely in OUaT.

Cora turns an unlucky bystander into a fish, assumes Regina's form, and transforms some never-named dead person into Archie's form (2.10).

Rumple turns Smee into a rat (cloud of black smoke) (2.11). This effect is reversed when he returns to the Enchanted Forest (3.17), although dreams of cheese linger.

Cora takes on Henry's form and finds Regina in her vault (2.12). She resumes her own shape with blue smoke.

Cora poses as the Blue Fairy when she talks to Snow (2.15).

Rumple removes and restores the Sheriff of Nottingham's tongue in the past (2.19) with a cloud of black smoke, and then takes it again and vanishes it in the present day with more black smoke. He also sinks Belle into the ground to restrain her in this episode.

Regina disguises herself as a fisherman to eavesdrop on Snow and Charming; Rumplestiltskin transforms Regina (blue smoke) so she can try to find Snow White (2.20). Noteworthy because her transformed self cannot use magic.

Regina turns a mermaid into wood (3.01).

Regina takes on Ursula's form to deceive Ariel (3.06).

With Rumple in hand, the Shadow points at Malcolm, who becomes Peter Pan (3.08) amid swirling green smoke. He returns to his old form when Rumple stabs him with the cursed dagger (3.11), this time with black smoke.

Walsh turning into a flying monkey (3.12) is evidently under his conscious control.

Regina turns a flying monkey into a stuffed toy amid purple smoke (3.13).

Zelena's overwhelming envy of Regina turns her skin green (3.16).

Rumple takes on Regina's form as a trap for Zelena (3.16); she stabs him in the neck, upon which he resumes his usual shape in a cloud of green smoke.

Zelena turns Walsh into a flying monkey (green smoke) (3.16).

Zelena takes on Ariel's form (3.17). She resumes her true form with green smoke.

Zelena appears to melt when water is thrown on her (3.20), and then reappears.

Ursula's form appears mostly human but variably tentacled (4.11).

Rumple takes on Hook’s form while dealing with Belle (4.14); no visual effect.

Zelena disguises herself as Regina after her escape (5.01).

Jafar uses a potion to take on the form of Alice’s father (OUaTIW).

Dopey turns into a tree when he ventures beyond the town line (5.02).

Emma turns Sneezy to stone (5.01). Regina changes him back (5.02).

Emma forces Merida to use a potion on herself that turns her into a bear (5.06). She is changed back by the anti-transformation powder Rumple uses on her.

Cora impersonates her husband Henry during a visit to Regina (5.12).

Evil Regina impersonates Archie to Emma and her family (6.05).

With Rumple's assistance, Jekyll perfects a serum (6.04) that allows someone to create a quasi-independent alter ego consisting of the qualities one would most like to suppress in oneself. This serum is later modified to physically separate the two halves of a personality (5.23). These halves can appear very different from one another. 

Gideon impersonates Aesop (6.15).

Jafar impersonates Prince Eric (6.15)

Transmutation
Rumple's ability to spin straw into gold presumably represents this type of magic. This is the first spell Cora learned from him (2.16).

Regina sinks Jefferson into the stone pathway, trapping him (1.17)

Rumple turns a man into a snail (and steps on him) with a black smoke effect. (1.19)

Regina turns the blade of George's guillotine into water (1.21).

Cora shapes stone walls into restraints for Hook (2.08).

Rumple restores the shattered teacup (2.22).

Rumple turns the fake Excalibur to dust (3.02).

Henry changes a stick into a sword (3.05).

Rumple sinks Roland into the ground to restrain him (3.18).

Merlin transmutes the flower stem he made into Nimue’s ring to gold (5.07)

Jafar turns Amara into a serpent and then the staff. Amara turns a chandelier into a multi-headed serpent (OUaTiW).