My lunch-break impressions of jd's 50 from the '90s link:
It's a more interesting list than it seemed at first glance. Quite a few I haven't seen, but I can't claim to be any kind of horror master, either. However, a lot of variety, and I think that's commendable. Whether all the films on the list can truly be considered horror are debatable, especially with the top 2, but I'm willing to let that be.
Some of the films I was maybe surprised (or not), but happy (definitely), to see on the list (again, horror pedigree aside for some): In the Mouth of Madness, Vampires, The Ninth Gate, Lost Highway, Man Bites Dog, The Dark Half, Exorcist III
Despite my dislike of Event Horizon, I understand many really love it. Hence, the only film I would certainly have eradicated from the list is Interview with the Vampire. (Edit: adgy-san sold me on knocking Sleepy Hollow out, too)
Very notable omissions, IMO (listed line by line due to one or two long parenthetical notes):
Audition (IMDB lists the USA release date as 11 June 2000, though, so for the same reason Henry is included, this may have been excluded),
Tetsuo (USA release date in 1992, so same logic),
Wes Craven's New Nightmare
Bride of Chucky (just a personal favorite; really well done IMO)
The Craft
Castle Freak
Village of the Damned (yeah, I know nobody likes this one but me)
a bunch of Godzilla movies, dammit
A few others as food for thought: Phantasm III: Lord of the Dead, Body Bags, Leprechaun, (the aforementioned) Hellraiser III: Hell on Earth, Flatliners, It, Leatherface: The Texas Chainsaw Massacre III, Tales from the Hood, Tales from the Darkside, Thinner, Species