I’m rather fond of the whole Seven Samurai homage storyline with Han and Chewie down on their luck, (having had their Rebel reward stolen by pirates) being enlisted by farmers on a bigger desolate hole than Tatooine to protect their small community from a local tyrant. And not just because Jaxxon was introduced. : )
I also liked The Wheel storyline, as it finally brought Vader back to the comic. Luke’s mishap while attempting to meditate using The Force was chilling. Han and Chewie being tricked/forced into a gladiatorial zero gravity arena to the death was great. (Many angry fan letters attest to fact they thought Han really died.) Wheel administrator and former senator Greyshade and his companion Master Com can be interpreted as the first robot/human couple in Star Wars, decades before Futurama did it.
The resolution of the Crimson Jack subplot (the leader of the pirates who robbed Han and Chewie back in issue 7) was also really good. Pirate lady Jolli had an interesting arc. Pity they didn’t keep her around to join the Rebellion or something. Plus, it would have given Leia someone to relate to with her scoundrel issues.
Last, but not least, the flashback issue with Luke and Biggs on Tatooine. Pity we never saw Skyhoppers take flight in the OT. And the SE doesn’t count. 😉