I don't often say this, but wow, what an incredible question. Going to take some serious thinking.
Just kidding. Here goes.
(Halfway through and I've realized that I'm going to have to do two separate lists: one for Horror, and one for not-Horror.)
Top Ten Best Doubleheader Movies - Horror
10) Near Dark and The Lost Boys. Two eighties vampire classics, giving you all the fun, blood and style that has been lost from the sub-genre.
9) Halloween and Halloween 2. Technically it's one continuous story. The second doesn't stand alone all that well, but does extend the joy of the first if watched together.
8) 28 Days Later and Dawn of the Dead (2004). Fast zombies changed everything! Now it's old hat, but these movies were ground-breaking, not only providing great entertainment, but also pushing the zombie genre into the mainstream.
7) Night of the Living Dead and Dawn of the Dead. The originals. Romero at his best.
6) Inside and Martyrs. Good luck getting through these two French horror movies back-to-back. Most can't handle this much awesome.
5) From Beyond and Re-Animator. The great Stuart Gordon does his Lovecraftian best with his signature sense of absurdist humour
4) Army of Darkness and Return of the Living Dead. The funnest (funnerriest?) of the horrory movies.
3) The Ring and The Grudge. You can do the two originals (Ringu and Ju-on) but for a full-faced scare explosion, do the remakes.
2) Friday the 13th and Sleepaway Camp. It's great, camp counselor fun and the endings aren't scary at all!
1) The Omen and The Exorcist. Right?
Top Ten Best Doubleheader Movies
10) Intolerable Cruelty and Burn After Reading. Lots of Coen's stuff to choose from, but I often pair these because they exemplify the brothers' ability to make strange, singular, little worlds that live and breath within their own rules of lunacy.
9) Dazed and Confused and Superbad. My two favorite coming of age movies. Totally different feels, yet the same feels.
8) Kill Bill Volume 1 and Kill Bill Volume 2. I hate to waste a spot on this super obvious one, but in my experience - because they came out in theatres a ways apart - people haven't often watched them together. I've only ever seen them as one entire film and have never been disappointed.
7) The Monster Squad and The Goonies. Wolfman's got nards + truffle shuffle.
6) Memento and Fight Club. Two 'have your mind blown' films from the same time period by two writing geniuses. I always bunch them together as two of the best first viewing experiences, as well as two of the best second viewing experiences, as well as two of the best films of all time.
5) Hero and Crouching Tiger, Hidden Dragon. Yimou Zhang's first American breakthrough is as beautiful as his other films, but with better fights. Then Ang Lee does his Chinese martial arts epic and teaches a few free lessons.
4) Ghostbusters and Caddyshack. Bill Murray connection, plus the fun and spontaneity of this era of comedic film.
3) Grosse Pointe Blank and High Fidelity. On the same actor train, these movies show Cusack at his rambly and lovable finest.
2) Alien and Aliens. This was nearly number one, and you know why. Both movies are great, so different they almost aren't even the same genre, and yet the main character's through line is outstanding.
1) The Godfather and The Godfather Part 2. Right?
Short Answer: Pairs of Cronenberg movies were number eleven on each list. Try to figure them out and win a prize! (The prize is my disdain.)