I can't decide on a outright favourite - so I will split into 2 catergories ! Vertical Scrolling & Horizontal Scrolling.......
Vertical scrolling would have to be Xenon II - great music, OK graphics and good playability. Nice enhancements such as humourous shop and weapons.
Horizontal would be Silkworm (predecessor to SWIV). I just loved the sound effects & destroying everything ! I can still here the Phwoooooom explosion sound now.