Tough - lots of great scores - here's my list:
1) Star Wars - especially Episode 4 - to this day it plays end to end like a major symphonic piece rather then a series of themes - no weak spots. New trilogy is not nearly as good end to end, but Dual of the Fates is a keeper. Lucas better be sending Williams a huge check every week for the rest of his life. This music made it all work.
2) The Mission - exceptional and haunting - rises above the very good movie it was made for - especially 'Gabriel's Oboe' and 'On Earth as it is in Heaven'.
3) Schindler's List - that theme hits me in the gut every time
4) LOTR - best fantasy score hands down
5) Indiana Jones - not as strong musically as the others, but so incredibly iconic
Honorable Mentions: Lawrence of Arabia (the granddaddy of epic scores); Glory (so darn good), Titanic (good, although it's oversaturated today); Willow (was best fantasy score until LOTR); Jaws (nuff said); Rocky (same); Chariots of Fire, Hunt for Red October, Jurassic Park...the list goes on...
EDIT: Ok, forgot E.T. and esp. Close Encounters - those have to be on the list somewhere...