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The newly released Holyday City (Unity) have offline progress, you can even earn a boost for being offline for at least 3 hours. It was bugged from the beginning, but it was patched yesterday.
There's also USSR Simulator and USA Simulator for Android. They're from the same developer, and are quite alike apart for some minor functions and wording. Offline earnings decrease over time due to corruption, which is removed by tapping a button in the game.
Lastly, there's Clicker Heroes (Kongregate), Tap Tap Infinity and Tap Titans. They're very alike and all have linear offline earings.