Salamander is almost a totally different game. Many many changes, when played on Expert it's the best version of the game imo, just a shame about the missing parrallax and voices.
Salamander just seems like a straight port of Salamander.
There are some special ports.
1943 Kai is huge, since it adds another 4 levels, which are even better than the Arcade Mode.
Darius Plus and Super Darius both have more bosses than Darius. Super Darius II is quite different than Darius II.
Bloody Wolf has a 2nd half added to the game (related to a story spoiler though, cannot say).
Street Fighter II has a legit versus mode (like all the other ports).
Cadash has a vastly different visual style.
After Burner II has a mode where you can edit the title screen balls.
Aero Blasters has different music and a legit ending.
Mr. Heli and Ninja Spirit both have PC Engine Modes.
Legend of Hero Tonma has a duck button, which makes the final boss a breeze.
Volfied has a vastly different visual style and level design than Arcade and Genny versions.