I've got the Amiga, SNES, Mega Drive and Master System versions on the original platforms, and I recommend the Master System version, to be honest. It's got the extra worlds introduced in an Amiga expansion pack (the Bitplanes levels, for example), plus it's got more levels than the others put together. I prefer the interface and the control method, even above the mouse-controlled Amiga version (which I always thought was too fiddly).
The 16-bit versions have prettier graphics and more sound, though.
EDIT: Just played the MS and SNES versions back to back - I got the latest Retro Gamer, too. The SNES version does indeed look a lot prettier and has a larger visible portion of the landscape, but the background sound will get on your nerves within 5 minutes. You can turn off the wind sound, but you can't turn off the heartbeat sound effect without turning off all of the sound effects. If you turn off everything you can't rely on audio cues any more. They're important to know when the opposition has created a knight or someone's fallen in a swamp. Oddly, the sound effect that should play when a swamp is created is missing from the SNES version.
The Master System version, despite only having two buttons, does a better job of the controls. It's also considerably faster than the SNES version under emulation.
