Only a handful have I seen more than once in the theater.
During the same run of the movie:
Moulin Rouge, three times. Once for me. Once with a friend who I knew would love it. Again for me.
Chicago twice, both by myself. Whale Rider twice, once alone and once with a friend.
Years apart: Gallipoli and Picnic at Hanging Rock, once when they each came out, and once at a Weir film festival.
Willie Wonka and the Chocolate Factory – three times (I think). Once, when it first came and maybe two other times when it was double-billed with another movie.
The Empire Strikes Back and Raiders of the Lost Ark – two times.
Back when I was working in a prison, one of the jobs I had for a while was watching the prisoners on movie nights. The prisoners were split up into four groups for movies and I had to watch each showing. So I’d end up watching the same movie four times in a single weekend.
One thing I found is that the plot holes in a weak movie become glaringly obvious when you watch it four times in a row.
Outside of work, I don’t think I’ve ever seen the same movie more than twice in a theater and twice would be rare. The most recent time was Toy Story 3. I went to see the regular version and then a few weeks later I had an opportunity to see the 3D version so I went again.
A very few movies twice, only one movie more than twice: The Longest Day, I saw it four times when it came out in the 60’s. It’s a very rich tapestry that bore repeated viewing, and was also very uplifting.
Roddy
Same here though it has to be into the high dozens. Of course, it really wasn’t about watching Rocky Horror, but partying in the theater with friends, so I am not sure if that actually counts. I remember seeing the originally Red Dawn at least 5 times in the theater because there wasn’t much to do that teenage fall and all my friends thought the actors were cute.
I can’t think of any specific examples but probably 3. I’d be hard pressed to name a movie I’ve seen in its entirety more than 5 times in any format. Even two in the theater is very rare, usually because I saw something by myself and then my wife unexpectedly decides she wants to see it.
I have a strong bias towards seeing something I’ve never seen before over going back to something I’ve already seen, regardless of how good it was.
Oh, I forgot about The Empire Strikes Back. My family was visiting my cousins in Ohio, and the adults dropped off all the kids (ages 9-12) at the theater to see ESB. They told us that if the movie ended before they got back, just to stay in our seats. So we did and ended up seeing the movie twice all the way through before our parents came back to get us. We didn’t mind.
Both of my multi-watched movies are Star Wars:
When it was re-released a local second-run theater was showing it for $1. I was a kid at the time and me and my friends went to see it almost every night for a two-week run.
Later, when Return of the Jedi was released I was working at a movie theater, mopping floors in the morning. I could watch all the movies I wanted for free and saw RotJ a few times a week for the entire summer. I also saw Private School more than a few times; Phoebe Cates was my first actress crush.
I’ve seen 2001 7 times in large rooms in public (as opposed to home.) Twice in Cinerama right after it opened, twice - in a row! - the the non-Cinerama first run, once in a revival, once at MIT in the movie program, and once at a Con.
Star Wars 3 times - twice first time through, once the re-release.
I used to go to a shopping mall in the 70’s after work, every Friday evening, to pay on my layaway at a store and just hang out after a hard week. And I went to see “Jesus Christ, Superstar” EVERY Friday evening - I think I saw it at least a dozen times. At least. (tickets were cheap back then, I loved the movie, duh, so…yeah).
More recently, I saw “Chicago” six times. “Rocky Horror Picture Show”, at least a dozen times over the years.
Back when I was young n’ cute and dating a lot, I was taken to see “Saturday Night Fever” AND “Alien” AND “Halloween” several times, with several different people! “Hey, want to go see that movie with John Travolta?” “Sure!” “Wanna go see that “Halloween” movie?” “You bet I do!” “That “Alien” movie is supposed to be…” “I’d love to!” 
I was easy! (not that way!)
Twice, four times:
The Breakfast Club: It just struck a chord with me (I was the right age at the time), so I paid to go see it again.
The Fellowship of the Ring: I saw it with my best friend the first time. Then I found out a coworker friend and her husband wanted to see it, but were having some money issues at the time and couldn’t justify the expense, so I took them to see it.
Revenge of the Sith: Watched it myself, then took my mom and stepdad to see it.
And I’m not sure if this counts, exactly, but I saw Star Wars once in 1977 (when all my friends got to go see it multiple times; my family just didn’t go to the movies very often). Then I saw the 1997 re-issue with the added CGI.
I saw 2001 twice in theaters. (So, that’s like 4002, right?)
Don’t recall them, but there must be others. Maybe some Disney film or some such.
I saw Star Wars 26 times in a theater back when it was first released.
IIRC, I’ve only watched one movie in the theater twice: Bloodsport.
City Slicker with Billy Crystal: 6 times. The point of finding the one thing that makes you happy was very important to me back then.
I saw Jurassic Park twice, but not through choice. A friend who was with me wanted to see it, but I had already seen it a week before. Seeing it a second time so close together is one of the reasons I don’t think it’s all that great a movie. I saw it a lot more objectively.
Six times each:
The Empire Strikes Back
Star Trek II: The Wrath of Khan
Why? They were just such great, amazing movies – they made me feel good every time, and before all of the options we have today, the only way was to keep going back. Now I just indulge by watching DVDs over and over again.
Four times each:
Silent Movie
Star Wars
High Anxiety (Warren Beatty/Julie Christie version)
Three times each:
Much Ado About Nothing (Kenneth Brannagh version)
Aladdin (Disney version)
Two times each:
Many other movies in the pre-DVD/Internet era
Six, I think - Star Wars when it first came out, in '77.
I was going to say that I’ve never seen a movie more than once in a theater but I forgot about Rocky Horror. I saw it maybe five or six times in '81 - '82.
Once only for me. I did see the RHPS at the drive in and at the theatre though.