I came up with this theory on my own back around 3x19, but I didn't want to share it with anyone until now. Sorry for the length, but I go into great detail to ensure perfect understanding, so please read to understand completely.
Reasons for Colours:
The normal colouring of the Dark Curse is a black/grey cloud with green lightning (as shown in 1x01, 1x02, 2x09, 2x17 and 3x19) which has appeared with both the Evil Queen's and Snow's curses. (I believe that the green lightning parallels the green vortex and lightning created by Magic Beans due to their shared ability to transport people to another world).
When Regina undid the First Curse, she generated magic using the Curse Scroll. She didn't cast a new curse, simply a spell that stopped Pan's Curse by putting her's into reverse, sending everyone back to EF (including Dr. Frankenstein and Jefferson). That's why the cloud was purple. (I also think that the scroll was magically recreated after the First Curse was reverted, which is how they were able to remember what was needed to cast the Second Curse).
Pan's Curse appears green for one of two reasons:
1. The waters in the well that share power with Lake Nostos (able to heal, strengthen, or return what was once lost) effectively strengthened the Dark Curse, removing Charming and Snow's true love factor from the equation and causing it to become unbreakable as stated by Mr. Gold. This caused it to change colour due it having been altered by the water.
2. The Dark Curse takes on characteristics of its caster (see below) and Pan's appeared green due to this.
The Dark Curse also taken on the characteristics of its caster (due to its magical interactions with the subconscious of the caster). The First Curse was violent and destructive as it spread throughout EF due to being cast by the Evil Queen; the Second Curse was more gentle, simply spreading like smoke (albeit with lightning) throughout EF due to being cast by Snow.
Creating Storybrooke:
Due to the Dark Curse's subconscious workings, it is able to create the perfect world for its caster as stated by Mr. Gold, which is why in the First Curse, SB appeared as it was due to being "created to service the Queen's wishes", why with Pan's Curse "you can count on something hellish", and why with the Second Curse SB returned to how it was before the events of 3x11 as Snow simply wanted to return everyone back to LWM, not wipe their memories and create a new life (but Zelena forcefully readded the memory loss factor by adding a forgetting potion to the cauldron).
Change of Casting Method:
Also, the reason that casting method appears different is due to the usage of Enchanted Hearts and the time of filming and writing episodes. When "Pilot" was made (much earlier than the rest of Season One), they hadn't created the Enchanted Hearts concept, so ripping out a heart simply killed the person (they simply continued this idea for 1x02). After they made the concept of Enchanted Hearts, they had to change the casting so that it would still be a sacrifice due to the victim being dead, so they made it so that you had to crush the heart into a cauldron of ingredients to kill the victim and achieve a sacrifice (the Wishing Well served as a large cauldron for Pan's Curse) as opposed to throwing an already dead heart into a fire.
Thank you for reading my super long theory (but it fits into OUAT doesn't it?).
Update: Hook's Curse appears different to the norm as his sacrificed heart was placed into a cauldron of an entirely different mixture, that somehow created a Dark Curse. This could be the reason why the cloud is purple. The yellow/golden lightning is from the dreamcatcher added by Emma to erase memories.