Old Republic era: I recommend the Tales of the Jedi comics, the KotOR games (particularly now that Team Gizka is just about done with their “fix” of KotOR 2) and comics, and the Darth Bane books. I happened to like them, but some people hate Drew Karpashyn’s writing and canon inconsistancies. He’s also the guy that wrote Mass Effect and its tie-in novels, so if you liked those I’d say give him a try.
Rise of the Empireera: I thought that Jude Watson’s books were great for young reader type books, and later books occasionally mention details from them, but they’re not necessary. I also like the majority of the comics released in this era, but there are a whole lot of titles here, too many to list before lunch It’s been a while since I read “Cloak of Deception” but I think I liked it, and there’s some good pre-Episode 1 setup. “Darth Maul: Shadow Hunter” is necessary if you want to read a lot of the Michael Reeves authored books, and I remember loving it but I’m not sure how much of that is because I have an unholy love for Darth Maul. The novelizations are a good back-up to the films, but you HAVE to read the one for Episode 3. In fact, just read everything by Matthew Stover.
Going into the Clone Wars subdivision: “Shatterpoint” becuase Matthew Stover is awesome. “Cestus Deception” was good, particularly if you like Asajj Ventress and Kit Fisto. “Yoda: Dark Rendezvous” was great. “The Clone Wars” novelization was pretty good, and “Clone Wars: Wild Space” was wonderful. Try the Medstar duology if you liked M.A.S.H., and Karen Traviss’s Republic Commando books if you like clones or the RepCom game.
Post-Clone Wars, still Rise of the Empire era: Here is where the legendary Darklighter comics go Also, the A.C. Crispen Han Solo trilogy (YMMV, since people accuse Brea Tharen of being a Mary Sue. I loved the books.)
Rebellion era: “Allegience” by Timothy Zahn. Just read anything by Timothy Zahn. “Shadows of the Empire” is a must-read. I also think “Truce at Bakura” is great, as are most of the short stories in the “Tales” books. And there are more wonderful comics here, though I have to point to the Rogue Squadron series as the shining star of this era.
New Republic era: “Luke Skywalker and the Shadows of Mindor” because despite the dorky title, Matthew Stover can frakking write. Much like Zahn, read anything with his name on it. All of the Rogue Squadron books by Michael Stackpole and Aaron Allston–feelings were mixed on “Isard’s Revenge” but I still liked it, even if it wasn’t quite up to snuff with the others. “The Courtship of Princess Leia” and “Tattooine Ghost” are great looks at Han and Leia’s relationship, and TG bridges the OT and PT somewhat. The Thrawn Trilogy, of course. “I, Jedi” and the Jedi Academy trilogy–if you don’t like Kevin J. Anderson’s writing, you can just read I,J but you’ll be missing out on some stuff. “Starfighters of Adumar” is hilarious, and a must-read if you like Wedge Antilles. I liked the Corellian Trilogy when I was thirteen but I don’t think I’ve read it in years and can’t speak to the quality anymore, but there’s some stuff in there that’s relevent to the NJO and Legacy books. The Hand of Thrawn duology and Union comic are wonderful. “Survivor’s Quest” is another Zahn book and PT-era bridge with Zahn-created characters at its core.
New Jedi Order era: “Vector Prime” is the start of it all. Some people say you can skip the next two, but I love Michael Stackpole so I’d say it’s up to you. The Agents of Chaos duology is kind of important, but the gist of it can be summed up in two words: Space Chicken. Balance Point is kind of important, but… eh. The Edge of Victory duology is important, as well as being a great look at both Anakin Solo and the Yuuzhan Vong. “Star by Star” is good and important. “Dark Journey” can be skipped, IMO. I recommend the Enemy Lines duology because they were written by Aaron Allston, and “Traitor” because it is both awesome and a Matthew Stover book. “Destiny’s Way” should probably be read, especially if you skip the Agents of Chaos books. The Force Heretic books are interesting if you like the Chiss, but can probably be skipped. It’s been too long since I’ve read it to remember if you need to read “The Final Prophecy”, and “The Unifying Force” is a must-read since it’s the end of the series, even if it was only “meh” IMO.
Legacyera: I have a hard time picking and choosing independent books here since it’s tighter-plotted. If you read the nine-book Legacy of the Force arc, definitely read “Millenium Falcon” and give the Fate of the Jedi books (or the one that’s out ) a try. And definitely try the Legacy comics–Cade is much less annoying after the first arc, I promise.