The Disney Food Blog has a cupcake challenge checklist. Obviously you can modify it, but it may be a good place to start. Your right though, the cupcakes are a perfect snack.
Yes, it's still there as of 08/18/18. It's in Roaring Fork, the quick service restaurant which is inside the hotel. I did not try it. Most days they only had one other cupcake in that restaurant, a Peanut Butter & Jelly cupcake which did not tempt me. I thought the selection was better at Contempo Cafe over at the Contemporary. You can take a boat there from Wilderness Lodge.
The Darth Vader cupcake at Backlot Express in HS was delicious and huge! My niece got one for free since it was her birthday and we all shared it. It was really good.