From Dark Empire II, I really liked a lot of the side story- Ossus comes to mind. The first Dark Empire ends in such a way that you can't really not continue it... but Dark Empire II isn't very good. Empire's End has no redeeming qualities that I can remember.
I really enjoyed the parallels betwixt Dark Empire and the Tales of the Jedi comics. Dark Empire II had some of that.
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I used to carry a bullet in my pocket marked 'KJA' since he used to be the guy who ruined Star Wars. (Guess which bullet I carry now?). However, Jedi Academy was only the beginning of the end and I can still enjoy it to some degree. If I had to prune the post RotJ down to the nubs, I think Jedi Academy would squeak in. It introduces a few long standing EU points- like the, SPOILER, Jedi Academy.