A Bookcase
While comics may not seem easily displayable in a bookcase at first thought, it might be a more elegant solution than you might expect. Not only does it allow for easy organization of the books (either by title, issue number or publisher) but it also allows for display of certain key issues so you can quickly browse your collection. Place all the books inside the bookcase as you would any book, spine out. At many points along the collection, place a book in front of the stacks, leaning back on them to display which books are in that section. This also allows you to display the most prominent books apart from your collection (for comic book bragging rights).
A Comic Rack
Talk to your local comics retailer or head online to find the same kinds of racks they use in the store. If you have the space for that kind of rack in your home, they are very effective at displaying your comics. Most racks have space to keep many issues of any particular series within the rack itself. Additionally, this gives you the option to put your most prominent books up front for clear display while storing the similar titles behind them.
The Wall Display
Put your comics you wish to display in a hard plastic case and find an empty wall in your house. Place adhesive fabric hook and loop fasteners on the wall and on the back of the comic case so that they line up. This will work for any length of wall, ceiling to floor. This comic display setup allows you to display your most prominent comics as well as decorate any room you hang the books in. Displaying your comics like this may not let you ditch the long boxes, but it sure will make people notice your collection when they walk into a room.
The Long Box Display
Short on cash or space? Those old cardboard long boxes could be the solution as much as they are the problem. Using hard plastic comic cases, put two strips of adhesive fabric hook and loop fasteners on the back of your comic case and the front of your long box. When you stack your long boxes, put them with the displayed comic facing out. Now you can display the most prominent issue of a series on the outside, and know just what is going to be on the inside of each box.