I'm still salty that the Special Edition versions of Monkey Island that I purchased on iPad like 10 years ago can't be played anymore. They weren't updated and LucasArts pulled the games from the store, which is a damn shame because they were the PERFECT examples of paid-games on iPad that were a great experience on the iPad given the point-&-click nature translating quite well to a tap interface.
The app I most regret losing in the 64-bit transition is Disney Animated [1]. App Of The Year in 2013, and gone completely a few years later...
[1] https://mashable.com/archive/disney-animation-app
I'm really mad at Half Brick for killing classic Fruit Ninja. I actually spent money on that game and on Jetpack Joyride, only to lose both sets of purchases. They suck.