I'm in the process of dredging up a couple old recommendations of mine.
First on the list is JLA: The Obsidian Age. This was the crowning point of Joe Kelly and Doug Mahnke's run on JLA, a few years before Infinite Crisis. A mega-arc so big it took two trades to complete, this story could have been even better than it was. A little more refinement, a little more thought during the writing process, and Kelly would have crafted a masterpiece.
*sigh* Ah, well. Even the flawed version that we got was tons of fun.
Time travel, sorcery, and a substitute JLA (consisting of Nightwing, Green Arrow, Major Disaster, the Atom, Hawkgirl, Jason Blood, Zatanna, and others) stepping in to deal with a present-day crisis while the 'regular' JLA was dealing with a threat in 1000 B.C...that period's version of a Justice League (hereafter dubbed as the "Ancient League"), based out of ancient Atlantis, and acting under the impression "our" JLA intended to destroy the world. I'm just going to post the beginning...( JLA v3: 7 pages from #66, 7 pages from #67, one from #70, two from #72. )