I don't have enough EU stuff read so I can only come up with around ten moments, most of which are in the prequel era.

10. Anakin Encounters Boba Fett--It is just very cool and very foreshadowing when Boba meets Anakin after the Battle of Xagobah in Boba Fett #6: Pursuit.
9. The Redemption of Asajj Ventress--Finally, after all those battles and supposed deaths, Obi-Wan finally convinces Asajj, or perhaps Asajj convinced herself, to turn back to the light.
8. Shaela Nur Turns to the Dark Side: Most readers probably don't know what I'm talking about. This dramatic moment is included in the story "Shadow & Light" in Tales #23. After the death of her love, Duron Qel-Droma, during the Great Hunt, Shaela takes the path of darkness, the last page of the story dramatically including the recalled warning of her master to never turn from the light.
7. Durge's Demise--Yes, the regenerative Gen'Dai dies in Star Wars Obsession (he deserves it for stealing HK-47's line) but in a very cool way, which includes the revealing of what he looks like beneath his armor and him getting caught in a huge ship explosion.
6. General Grievous's Debute: There's just one thing to say about Clone Wars Chp. 20: Awesome!
5. Bastila On the Dark Side: Bastila Shan turning to the Dark Side was one of the most dramatic moments in KOTOR, Revan choosing which side to take being even more dramatic.
4. Quin's Return to the Light....Well, he was always technically on the Light Side but that's not the point: I refer to the moment in the recently released Republic #76 in which Quinlan Vos finally reveals how he's tricked Count Dooku the whole time so he can find out the identity of the second Sith Lord. It was quite the dramatic moment.
3. The "First" Battle of Yavin IV: Anakin knocking Asajj Ventress off the cliff of the Massassi Temple was a great moment. Seeing him attack Ventress with a red lightsaber was very foreshadowing and the flashes of Obi-Wan, Yoda, and Qui-Gon were a nice touch.
2. Vision in the Tunnel: We all know that I'm probably the most continuity-obsessed person on this site but despite it technically never happening, Anakin's vision in the tunnel on Nelvaan was one of the most haunting and goosebump-inducing moments in EU history.
1. Revelation: I thought the revealing of the player being Darth Revan in KOTOR was the best EU moment. Not only did this twist almost stand up to Darth Vader being Luke's father but it was also extremely well-executed, compiling all the hints in the game.