I have a soft spot more for the John Williams of yesteryear, when he was known as Johnny, and with that, I would have to say my favorite score of his is a little-known comedy/crime caper from 1967 called Fitzwilly, which starred Dick Van Dyke and Barbara Feldon (away from Get Smart for this one). It's a transitional score which, on the one hand, evokes all the light comic scores he was doing, such as Penelope and How to Steal a Million (Williams was afraid of what Stravinsky would have thought of it, as he came to the film's premiere), and fortells the coming of the scores he would do for the Home Alone series, Harry Potter and Catch Me If You Can. Even the film's song, "Make Me Rainbows" (lyrics by Alan and Marilyn Bergman) is a precursor to his love themes from Star Wars and Superman.
My second favorite Williams score is for Brian DePalma's The Fury, their only collaboration. It's a shame, as Williams evokes two of his mentors, namely Bernard Herrmann and Franz Waxman, and giving DePalma one of the best scores apart from those Herrmann delivered for Sisters and Obsession.
My third favorite is another little-known film, a 1965 war film entitled None But the Brave, the only movie Frank Sinatra directed. Ahead of its time, this film dealt with a US Marine unit sharing the island (sort of) with a detachment of Japanese soldiers. Some of the music for the action scenes are quite good, setting the stage for Williams in later years to deal with Spielberg's take on WW2. Of the three scores I mentioned, this is the only one that I believe did not have a soundtrack album issued.
That said, I do love his later scores, but these, along with films like Diamond Head and The Killers, as well as his television scores for Irwin Allen, set the stage for the John Williams we all know.
By the way, he also composed a very dark and dramatic violin concerto that deserves more performances as well.