The standalone version of Shinobi is the arcade version too. But Sonic's Ultimate Genesis Collection apparently has the arcade versions of Altered Beast and Shinobi as unlockables.
Someone in a comment section on NintendoLife mentioned this site. Seems like a really good resource for DLCs, exclusives, or hard to come by physical games. Wii U & 3DS eShop Shutdown Exclusive Games, DLC, and Features List Thread [Deadline: March 26] | ResetEra
Shovel Knight Treasure Trove (3DS) for $4.49 is an amazing deal if you don't already have it. Includes the main game and all the expansions. The 3D in the game looks great too.
The Wii Virtual Console versions of Resident Evil 4 and Resident Evil Umbrella Chronicles is once again on sale for $4.99 each on the Wii U eShop, if anyone's interested.
If anyone's interested, there are 3 Wii Virtual Console games on sale on the Wii U for $5. All Capcom games: Resident Evil 4, Zack and Wiki, and RE Umbrella Chronicles. Just saw it today, so not sure if there set to end tomorrow or not.