Many on my list have been mentioned already, and I'm sure there are many more that are not popping up just now, but these are stories I'm pretty sure I'll never forget.
HOMECOMING
THE OUTSIDERS
INVISIBLE LISSA, Natalie Honeycutt
BLUBBER/STARRING SALLY J. FRIEDMAN AS HERSELF/TIGER EYES/DEENIE
VERONICA GANZ/AMY AND LAURA, Marilyn Sachs
Although I'm not sure these haunt me in the way you mean, because there are some books that make me feel what mc is going through so keenly that I walk around in a haze and wonder if perhaps I am on drugs [GO ASK ALICE] or autistic [THE CURIOUS INCIDENT OF THE DOG IN THE NIGHTTIME] and just don't know it...but the list above haunts me in that I still remember lines from most of them, or Davey's eyes (or Sally's rose) from the cover, or think of Sammy every time I say 'good-o'...these stories have soaked into me; I can remember where I was when I read them (or where I wasn't...first day of school in Florida with too-thick white socks and penny loafers while all the other girls wore sandals). So if that's what you mean by haunt, then, yes, these books haunt me. And thank God for it. What a gift (and what a great thread!).