Galaxy Guide #8: Scouts and GG #11: Criminal Organizations pop into mind immediately. Also, I did enjoy the Spec Force Handbook. Some of the background info in the Corporate Sector Guide was good, too. Beyond that, most of the other stuff I have is alright, but not as good as the aformentioned books.
I tend to use just about all of my old D6 material in some way or another. The best books well I like the Imperial and Rebel Sourcebooks. I also like the Pirates and Privateers book as it gives pricing on material and what it the bountys would be for rebel privateers. Wanted by Cracken is excellent supplement for bad guys..
Galaxy Guide #8: Fragments from the Rim! Best. Book. Ever.
Details some of the rimward planets, as well as how to run a Special Operations (as distinct from Special Forces) campaign. The terminology guide at the beginning is hilarious. *sniffle* I miss that book.
The central cluster of West End books describes the Rebellion era in detail that hasn't been duplicated elsewhere: Star Wars Trilogy Sourcebook, Special Edition, Star Wars Sourcebook, Imperial Sourcebook and Rebel Alliance Sourcebook. Past those, the more specialized sourcebooks and adventures all have something to offer, but it comes down more to personal taste.
I don't really play any Star Wars D20, but played a lot of the WEG version of star Wars for years.
My favorite supplements that may be useful to you:
The Corporate Sector Sourcebook
The Dark Empire Sourcebook
and there was this really cool book that was a compilation of fan designed equipment. I cannot for the life of me remember, because I sold all of my Star Wars stuff last year... Maybe someone else can help you out with the name, but there were many really cool devices in there...