At this point are Gwen Stacy and Uncle Ben still the only "big" characters still dead after a long time?
If Uncle Ben counts then Martha and Thomas Wayne along with Jor-El and Lara-El are still counted among the dead. Maria Castle and the kids also still dead.
I know those are all "origin specific" but since Uncle Ben is included that would count.
I think Gwen is a good example to go with when asking what character(s) is/are still dead in comics NOT tied to the need for their to be an origin story.
Ben Reilly...again after Spider Island.
Doc Ock has died....again, sort of.
Jason Macandale is still dead right? Jack O'Lantern/Hobgoblin
Karen Page(unless she's back in Waid's DD run, I don't know)
Gabriel the Airwalker(2nd Herald of Galactus)
Marlo, Rick Jones ex-wife?