Basically for me the EU ends with the Thrawn Duology. I like Ben Skywalker, and Luke and Mara getting together but everything else i pretty much hate. Was the Bantam era perfect far from it. Still prefer it over Del Rey, Superweapon of the week and all.
In my opinion, ending the EU with the Hand of Thrawn Duology can be a respectable choice, but I personally don’t agree with it. While I don’t like what they did with the NJO and subsequent works, at the same time I also want to see Luke at the head of a functioning Jedi Academy, and what they did in the Jedi Academy Trilogy was not enough for me. So, I prefer to end my personal EU timeline with the Young Jedi Knights series. The plots developed in that series are pretty good, the power levels are not absurd, and the Galaxy is at peace at the end of the story, with the clear implication that the new generation of Jedi will eventually replace the old, and will help to maintain peace and justice throughout the Galaxy for several millennia.