THE THRAWN TRILOGY, as that's where it all began. Michael Stackpole's I, JEDI is also very good. If you're down with space battles, the X-WING series by Stackpole and Aaron Allston is also good.
THE CORELLIAN TRILOGY was decent, but was very Han Solo-heavy, so you might want to avoid. It does influence a few of the following books, however. Most of the original line (published by Bantam) are disposable, and you'll want to steer clear of anything written by Kevin J. Anderson. THE HAND OF THRAWN duology might be worth a look at it shows the New Republic and the Empire making peace, which is important for later books.
THE NEW JEDI ORDER is a tricky one to recommened. It's huge - 19 books in length - and is a mixture of very good books (TRAITOR is the best, followed by STAR BY STAR and DESTINY'S WAY), quite a few okay ones (most of the rest) and some that are terrible (BALANCE POINT, DARK JOURNEY). Because it's one big story it's difficult to read books in isolation. I'd say the whole thing is worth it just to read TRAITOR, which is my favourite STAR WARS novel of all time.
Most of the later books I have a much more mixed critical reception. It was in that era that Karen Treviss became a popular author and started derailing the whole series: Treviss is a massive Boba Fett and Mandalorian fangirl, and makes books all about them when they have no right being here, even in the middle of multi-volume series. She's also outspoken in her belief that the Jedi are fascist nutcases and makes the Jedi seem weak and feeble in her books, outclassed by her Mandalorian ubermensch. She's actually not a bad writer, but she was definitely a bad match for STARS WARS and was dropped mid-series in her REPUBLIC/IMPERIAL COMMANDO books. Happily, she's being replaced by the far superior Stover.