I did mention that there were exceptions (just edited the post, actually), particularly during the period where the shows were exclusive (which is what you're talking about), but the majority of shared pay-per-views (SS, SummerSlam, RR, and 'Mania) eventually came to feature Raw main events. IIRC, the SmackDown main event headlined SummerSlam '02 (Rock v. Brock), Unforgiven & No Mercy '02 (Brock v. Undertaker), No Way Out (Rock v. Hogan II), and WrestleMania 19 (Brock v. Angle). But I can't seem to remember anything after that, save for Survivor Series '06 (Batista v. Booker).
Survivor Series '02 (Elimination Chamber), Armageddon '02 (HHH vs. HBK), and Backash '03 (Rock v. Goldberg) were all Raw main events. And after that you have SummerSlam '03 (Elimination Chamber), Survivor Series '03 (Goldberg v. HHH), 'Mania 20 (HHH v. HBK v. Benoit), SummerSlam '04 (Benoit v. Orton), SS '04 (Team Orton vs. Team HHH), 'Mania 21 (HHH v. Batista), SummerSlam '05 (HBK v. Hogan), WrestleMania 22 (Cena vs. HHH), SummerSlam '06 (Cena v. Edge) were all main evented by Raw wrestlers. SS '05 doesn't count for either side since that was SmackDown vs. Raw.
So in the vast majority of shared pay-per-views during the Brand Split (when it was actually split) were Raw dominated, and that period was the most important SmackDown! could ever be. There've been a couple SmackDown main events since then (SummerSlam '09, Hell in a Cell '10), but the same has proved true after 2007 as well.