Like the most film-music lovers I have a fair number of Jerry Goldsmith's horror scores in my CD collection. The music he composed in this genre has never ceased to amaze me with its use of innovative orchestral techniques and the incorporation of demanding avant-garde harmonies.
I'd have to list my favourites (in no particular order) as
The Mephisto Waltz
The Omen Trilogy (especially III)
Coma
Alien
Poltergeist I & II
As others have mentioned earlier, Christopher Young seems to have carved a real niche for himself with some equally inventive scores in this genre: I loved Hellraiser I & II and also his work on the two Grudge movies I found impressive.
What with film music being so diverse in its sources of influence it'll be interesting to see where things will be heading next for horror scores - whilst browsing some music pages on the monster that is Myspace I did come across a score in progress that seems to be looking back to the 1970's in terms of it's overall abrasive sound and instrumentation - although it seems to be for a direct to DVD release the tracks posted are pretty impressive and probably worth a look - the movie is called The Legend Trip
