First off, this is a very subjective question that will ultimately boil down to personal preference. I will offer you my opinion along with the reasoning behind it, but you may decide that another method is best for you. I store my chips in cardboard flips with mylar windows which in turn I insert into vinyl album pages that I store in albums.
I chose cardboard flips with mylar windows instead of the transparent vinyl flips. The vinyl flips that are nice and flexible contain PVC, which gives the vinyl its flexibility, but which also reacts with the inks in some chips and causes the ink to transfer to the inside of the flip. The ink can then can be transfered back onto the chip (or worse - onto another chip) as it rotates in the flip over time. This phenomenon is called "bleeding" can can ruin your chips (it is especially a problem with the red $5 chips). Now, there are non-PVC flips, but they tend to be brittle and crack if handled too roughly. To avoid the bleeding and brittleness, I chose the cardboard flips with the mylar windows. My chips are safe from bleeding and I don't have to handle them with kid gloves.
Some people staple the flips, but I like to be able to handle and touch the flips without having to ruin the flip, so another trick that I picked up from a club member is to seal my flips on the bottom corners with little white address labels that can be picked up at any office-supply store. This way, I can still remove the chips from the flips and handle them if I like.
I buy my albums at my local Sam's Supercenter. I can get a very nice and black nylon binder with a zipper (to keep anything from falling out) that will hold about 15 pages full of chips (roughly 180 chips). The binder also has all sorts of neat little zipper pouches and pen holders and even a notebook to keep up with my trades. It's very efficient to have when traveling to a trade meet. I can keep my business cards, address labels, envelopeps, stamps, etc. handy in there as well. Plus, it costs me all of $7 at Sam's, so with a dozen vinyl pages, the total for the binder comes to about $14.00.
Another plus about using the cardboard flips is that they fit very nicely into the long chip storage boxes when your collection grows to large to store in binders. The boxes are cheap as well - or you can even store the flips in boxes of your own because the flips will keep them nice and orderly inside.