Shockwave's command started in issue #5 and cedes command to Megatron again in issue #19. His leadership of the 'Cons lasts until issue #25, when depressed about the fact that Prime died in #24 and he didn't do the killing himself. He 'apparently' kills himself by blowing up the Space Bridge. Megatron doesn't officially command anything after this, even when he reappears on Cybertron at the end of #56.
Leadership of the 'Cons after his disappearance in #25 seems to jump from Shockwave, Ratbat, Scorponok, and finally Bludgeon by the end of the series.