Color me excited about this marathon. I think it's a great opportunity for people to discover movies they would have never looked twice at, simply because they're anime.
Akira (1988) - A milestone in the history of animation. No marathon would be complete without it. Akira's echoes can be felt in nearly every anime that follows it.
Memories (1995) - Three short films collected together, each with a different visual style and tone. It really illustrates the breadth of this genre.
Ghost in the Shell (1995) - One of the first anime films to appeal to the unfamiliar fan, and helped bring anime to the US. It's plot can be convoluted, but it (and it's sequel Ghost in the Shell II: Innocence) raises intelligent questions about identity and what it means to be human. It was also one of the first films to successfully blend computer and cel animation.
Cowboy Bebop: The Movie (2001) - Based on the series of the same name, Cowboy Bebop is simply a beautiful movie to watch. The opening credits alone are a testament to the talent of the artists who worked on this film. It's a lively movie that captures what makes the series great including the sci-fi noir tone and a soundtrack to fall in love with. It's lighter than a lot of the other movies listed, kind of Japan's version of a big summer blockbuster (if only our own summer blockbusters were this good).
Metropolis (2001) - Adapted from the 1949 manga (Japan's version of a comic book) it is also an expanded and reimagined take on the Fritz Lang film of the same name. It explores the relationship between robots and their human masters as well as themes of class and politics. It's rich in visual detail, and while the story can be confusing, the ending is powerful and heartbreaking.
Millennium Actress (2001) - Because it can't all be futuristic dystopias and robots. This movie uses the art of animation to it's fullest, the variety of artistic styles enhancing the narrative. The movie is a journey through Japanese history, with the actress and her memories as our guide. Poignant and subtle, this is a movie made for cinecrack addicts, no matter what their opinions of anime.
The marathon should also include at least one Hayao Miyazaki film, of which there are many. Each film has a different strength and appeal and every anime fan has their personal favorite. There are the ecological epic fables (Nausicaa of the Valley of the Wind, Princess Mononoke), the quiet childhood fantasies (My Neighbor Tortoro, Kiki's Delivery Service) and the ones in between (Spirited Away, Howl's Moving Castle, Castle in the Sky, Porco Rosso). I would agree that Miyazaki deserves his own marathon, but all of the films display Miyazaki's great imagination and world-building skills, so no matter what film you choose, you will be able to see why he is such a grand figure in the animation world.
(Other great anime films include: Grave of the Fireflies, Perfect Blue and Ninja Scroll)
On the Sub or Dub? front, while a few of these films have great English-language tracks, the majority of anime does not. It would best to watch all of the films in their original Japanese with English subtitles.