An organized baseball card collection is a more fun and more valuable collection. You should do your absolute best to come up with some type of system that works for you in helping you keep your collection organized. There are more and more fancy tools to help you do this, but the key is to just do it.
I like the software that Beckett uses on their web site called “My Collection”. The “My Collection” tool is a great way to keep track of the cards that you have and it also displays the current book values of each card and of your entire collection. Using the “My Collection” software you’ll be able to see all of the cards that your favorite player has, all of the cards of a particular set you are working on, online checklist, etc!
There is other baseball card collecting software available or if you’re good with excel you can create your own. I personally used to keep all mine in a Microsoft Access database. It got too hard to type in all the individual cards when I bought a set of 700 cards so then I switched to using http://www.beckett.com/. Just point and click then its added. There are also some software packages you can buy as well like The Card Collector or Sports Card Tracker.