Rogue Squadron series by Michael A Stackpole (Rogue Squadron, Wedge's Gamble, Krytos Trap, Bacta War) - these are fairly good, although Stackpole isn't the best author in that he doesn't really bother fleshing out all of the characters in the squad - seriously some of them have about 2 lines and that's it. You really should have started here, chronologically.
Wraith Squadron series by Aaron Alston (Wraith Squadron, Iron Fist, Solo Command) - generally considered the best series in the Star Wars EU alongside Thrawn. Unlike Stackpole he's very very good at writing characters, and none of the dialogue feels forced or contrived. Also Wes Janson is awesome.
Then there's The Courtship of Princess Leia, which was really really terrible, then there's the Thrawn Trilogy.
Isard's Revenge by Michael A Stackpole (standalone) - felt rushed and didn't really add anything except for a few cool nods to the TIE Fighter game. Take it or leave it, it's not connected to anything else really.
Jedi Academy Trilogy by Kevin J Anderson (Jedi Search, Dark Apprentice, Champions of the Force) - Decent, but no where near as good as Thrawn.
I, Jedi by Michael A Stackpole - again, felt rushed. Apparently the one Star Wars book written from a first person point of view.
Starfighter of Adumar by Aaron Alston - for many this is the pinnacle of Star Wars EU writing.
Black Fleet Crisis Trilogy by Michael P Kube McDowell (Before the Storm, Shield of Lies, Tyrant's Test) - Generally not that liked, I absolutely loved it and put it alongside Thrawn and Wraith trilogies. A slightly different style of writing - a lot harder military science fiction than the rest of the books listed here, though as I said I may be the only person that likes this (Lucas Licensing certainly didn't because basically nothing from it appears anywhere else
).
Hand of Thrawn Duology by Timothy Zahn (Spectre of the Past, Vision of the Future) - very very good until about a third of the way into the second book, where it all just sort of stagnates.
Survivor's Quest by Timothy Zahn - Acceptable, if far fetched.