My view is for a purchase as important as this, you will want it configured exactly to your specs. Otherwise, down the road, you'll be sorry. Having said that, depending on what you want, I'd order through the web site. I doubt the stores would have a broad inventory to cover the various ways a base computer can be set up.
I just changed into a Seagate 320 GB 7200 rpm hard drive that I bought through OWC. My 2007 MBP came with a 120, 5400. It was easy to do. I earlier upgraded to 4 GB of RAM from Crucial.
Without a doubt, the one thing you need to buy at the outset is Apple Care. It will pay for itself when something goes inexplicably wrong. One other thing, buy the biggest and fastest you can afford. You never know how your computing needs will change once you get into a quality product from Apple.
Good luck.