The Revenge of Shinobi has been released for many systems, this page is a list of them all.
Dreamcast
The Revenge of Shinobi is featured as one of the 12 games on SEGA Smashpack, a collection released for the Dreamcast in 2001. The majority of games on this collection are Genesis titles, and they all suffer from poor sound emulation, resulting in horrible sounding music.
MEGA-TECH
The Mega-Tech was an arcade system which played Genesis or Master System games. Players could select one of 8 titles and play them for, from what I understand, a limited amount of time before needing to insert coins to buy more time and continue. The Revenge of Shinobi was one of the games available, however I'm not sure which revision was used. These arcade machines were only officially released in Europe and Japan. Picture from The Arcade Flyer Archive.
GENESIS/MEGA DRIVE COLLECTIONS
The game was later released on several compilations in the early to mid '90s. In Europe, it is on Mega Games 2, Mega Games 6 and Mega 6 Vol. 3. In America, it is one of the games on the 6-Pak collection. In Brazil, it is on Mega Games 10. These collections all use Rev03.
PC
Smash Pack was released in 1999. Somehow, SEGA included a prototype version of the game on this collection, which is covered here. Apparently whoever out together the box art wasn't that bright either, as they used a picture of Shinobi II: The Silent Fury -a Game Gear game -by mistake. The manual for this mentions that you can select any level at the start of the game, so whoever wrote it clearly wasn't aware that something was wrong.
Many years later, SEGA released the game for a second time for PCs, this time using the correct, final version. This version is available to download via Steam. There are also rumors that this version will be included on SEGA Mega Drive Classic Collection Vol 5, the fifth European-exclusive collection for PCs.
PLAYSTATION 3
The PS3 version was released in 2012. It features trophies and a new trials mode. This version was used in the Alex Kidd & Co collection for the Xbox 360 (see below).
SEGA CD
SEGA released two "SEGA Classics Arcade Collection" titles in America, and both had a version of The Revenge of Shinobi on them. The first collection contain four games, whilst the second collection has five. In Japan, only the four game collection was released, whilst Europeans only received the five game collection. The version of the game on them is the same as Rev03, but Joe makes a different sound whenever using a ninjitsu attack.
WII
The Wii version was made available for the Virtual Console in 2009. This version had several slight changes made to it, which are covered here. The Wii version would later be used for the Xbox 360, Playstation 3 and the second PC release.
XBOX 360
The game was part of Alex Kidd & Co for the Xbox 360, and comes with Alex Kidd in Miracle World and the arcade version of Super Hang-On. It costs 800 Microsoft points. I think I speak for everyone when I say that a Mega Drive Shinobi collection would have been a far better idea.