Gotta go with The Haunting. Just amazing atmosphere.

The Haunting scared the heck out of seven year old me. Purely suspense and atmosphere, nothing graphic on screen. Having Shirley Jackson's novel as source material for a master like Wise was a great match.
This scene in particular freaked young me out.

I got to see it as a grown-up at a big-screen revival showing. It's really effective when you encounter it for the first time on the big screen (Even if you've read about it and know basically how it ends). It's a beautiful example of how you don't need gruesome, bloody imagery to make a scary movie. As a reviewer once put it, when you think there might be a ghost nearby, you're not afraid because you think the ghost is about to pull a knife. It's not about scaring the primitive "lizard brain" part of the mind. "The Haunting" captures that more subtle quality.

The early movies he did for Val Lewton were effective chillers too.

"Star Trek: The Motion Picture" was a good try, but there's a reason why "Wrath of Khan" is so much more popular.

I've heard that "Audrey Rose," not mentioned here, was a great movie, but didn't find it one of his best when I saw it.