The thing to keep in mind, first and foremost, is to store them in containers that were made specifically for this purpose. You want to preserve the paper. That means anything you use for cardboard or paper storage (ie, comic books) should be lignin-free and acid-free. If you use plastic storage, it should be PVC-free.
Another thing: Store your collection in a climate controlled environment, stored away from direct sunlight. Please don't put your comic books up in your attic or shed!
You have a lot of different choices as far as choosing items in which to store your comic books. For most comics, plastic sleeves as well as acid-free resealable bags are perfect. For especially valuable comics, you should consider plastic boxes made especially for this purpose. If there are any adhesives involved in sealing these bags, you must make absolutely sure that the tape doesn't touch the books.
Plastic comic book boxes can be found at collectibles shops or storage and organization stores. As an alternative, you should be able to find Mylar comic book sleeves that have special cardboard backing. This makes the container a little more sturdy, better protecting your book.
Now then, assuming you've stored all your most valuable books in individual containers, it's time to consider how to store the rest of your collection. There are many boxes you can buy online or at comic book shops, and they generally come in two sizes - short ones hold about 100 books, and the longer ones hold about 300 comic books.
Before you even store your comic books, though, you probably want to think about how you want them organized. The most common way to organize comic books is by title, then in chronological order based on the date of publication. Whether you want to read them in the future or sell them, you'll be able to quickly and easily find any comic book you want in an organized comic book storage system.