Well, one way is to categorize them based on the publisher or the era they were released. Also, using shelves or boxes labeled appropriately helps keep them organized. It might take some time initially, but it's worth it for easy access later.
First, decide if you want to group them by characters, storylines, or artist. Then, get some storage containers and label them clearly. This way, you can quickly find the comics you're looking for without a hassle.
You can start by sorting them by genre or series. That makes it easier to find what you want.