The ending of the series is pretty heartwarming. Sure, all the characters go their separate ways, but they promise to see each other again (which they do in the bonus chapter) and in the end, everybody is happy. The best part is seeing that Kenshin and Kaoru at least are now Happily Married and have a son.
It's a darker moment, but Hoji reuniting with Shishio and Yumi in hell. He's just so happy.
Live Action Film
Kaoru shattering Jin-e's lethally strong Shin No Ippo technique which froze her lungs through her sheer love for Kenshin to stop him from becoming a murderer again to save her life:
KENSHIN DON'T!! Don't become a manslayer again... Please don't kill him... Kenshin... For those who died by your blade... And for everyone whose life... you have saved.... Please don't kill him... A sword that doesn't kill.... A sword that can protect.... For this new age.... of peace... Isn't that what you fought for?
The ending deserves a spot here surely. After Kaoru is rescued by Kenshin, she wakes in the dojo with a start. She then looks around, finding Sano asleep in the adjacent room, while Megumi and Yahiko are in the kitchen, but Kenshin is nowhere to be seen. Panicking, she assumes he's left the dojo to wander once more and rushes towards the gate (not bothering to put on her sandals to boot). But she stops when Kenshin appears at the gate with the day's groceries. And when Megumi (who gently admonishes Kaoru for jumping to conclusions), Yahiko and Sano join them, the following exchange occurs: