I would say that the two most valuable games consistently would be:
Moonstone (avg. 100-120USD)
Zak McKracken (avg. 60-80USD)
I have only ever seen 1 copy of ninja gaiden for amiga on ebay and it sold for over $500, I think that is the highest single sale I have ever seen of an amiga game.
I should state that I own about 400 complete boxed amiga games and many more c64 disk games too... I think only Jerry Kurtz from lemon64 has me beat on the size of his amiga + c64 game collections of active scenesters.