Secret Wars was a lot of fun.  Age of Apocalypse was my favorite thing about X-Men in the 90's.

Onslaught is by far my least favorite crossover - killed my interest in X-Men until Morrison's NewX-Men.

Is the Star Trek episode Savage Curtain the one with Abe Lincoln? 
If memory serves it was indeed a very similar premise - all-powerful entity staging a contest of good vs. evil.

I'd like to see in hardcover:
Avengers By Perez/Byrne (181-202)
Alpha Flight by John Byrne Omnibus
Excalibur by Claremont/Davis Omnibus Vol. 1

Shazam by Don Newton