Instructions
Buy several large binders, preferably D-ring, and card collector sheets. Collector sheets work particularly well for Yu-Gi-Oh.
Organize your cards before you put them into your binders. Typically, keeping the cards organized by type (Creature, Spell and Trap), then further broken down by casting type or effect works the best.
Place the cards in the sheets, giving each card a full column. If you only have one of a card type leave the rest of the column empty for when you get more of the card type. If you have more than three of a card, only put three in the page and leave the rest to the side for trading.
Research special packs and Starter Decks for special cards that you can't get anywhere else. For instance, when the "Yu-Gi-Oh:The Movie" came out there was a special pack that contained cards relating to the movie. Since each pack was the same, you could get three packs and have a full set.
Keep a spare pile for trading and gifts. The best way to get a friend interested in Yu-Gi-Oh is to give them a set of cards. If those cards happen to be ones that you can't get rid of then you both win.