Exile AGA was a total rehaul graphically. Looks very nice, but the game is not really better. I think I prefer the smaller sprites of the original -- they look great to me!
Second Samurai had some much nicer backgrounds in AGA, and other small differences in the levels. Nothing major.
Things like Simon The Sorceror look nicer, Transatlantic is faster & has more colors, Sabre Team was much faster... I think UFO had quite a big difference too?
Zool 2 and Robocod have some new backgrounds and music, I think, and may even have a couple of extra levels.