Even after her death, Tomoe is still remembered and played a part in the plot of the jinchuu arc. Kenshin first visited her grave in manga #18. He placed flowers and burnt some incense for her. Then he prayed.
It is important to note that Enishi (Tomoe's brother) sometimes sees the ghost of his sister in his head. At first Tomoe's image was smiling, but then she frowns.
Tomoe visited Kenshin in his dreams in manga #26. She said that she was happy. She then told Kenshin that if he is happy then the Tomoe inside him will be smiling. This also applies to Enishi.
After the defeat of Enishi, Kenshin and Kaoru went to Tomoe's grave and pray for her. Kaoru said thank you.. for indirectly saving her life. Kenshin too, said thank you and good-bye.
