Thor Dis-Assembled. A Ragnarok that would've probably made Kirby proud.
It ruined the relaunch for me because it raised the bar so incredibly high.
New Mutants #37 (with #38 to end on a happier note, and it has a cool cover to end on). The Beyonder kills the New Mutants and brings the Sienkewicz era of the team to an end. After these two issues, I couldn't read New Mutants anymore. Between the story and the new direction that started afterwards, it just felt 'finished' to me.
Micronauts. Both series had good endings.
The first volume had them reach the goal of defeating Karza and freeing the Multiverse.
The second volume had them reach the end of their stories and find peace.