Upgrades such as flooring, countertops, window coverings, etc are all part of the builder's profit center. Sometimes you'll get decent pricing on these, sometimes not. You'll need to have some idea as to pricing of these items before you go to their design center.
Builder-affiliated lenders are typically very competitive, but it doesn't hurt to shop around. If you find a better rate elsewhere, see if the builder's lender will match it. If you do use an outside lender, it's likely that the builder incentives will go away, and you may have potential penalties for not closing on time, so be sure to weigh all of your options.
If you buy directly from the builder, you should have at least a 1-year warranty for any issues that may arise during that time frame. If you buy from a regular seller, the builder will not always honor this 1st-year warranty. Either way, you can always purchase 3rd-party home warranties to protect your home. I always advise my clients to have an inspection just prior to the expiration of the builder's home warranty so they can request the correction of any outstanding items before the builder's warranty expires.
Don is correct in saying that using a realtor for your purchase is important. The builders typically have realtor commissions built into the advertising budgets, so you won't save anything by going in on your own. Do remember that if you use a realtor, you must go into the sales office with your realtor for your very first visit, so don't go wandering in there alone. A realtor can help you get all available incentives and discounts, and assist you through the loan process as well as answering any questions that may arise. Remember that the people in the builder's sales office work for the builder, not for you!
Sometimes the builder is able to line up especially good financing. Then, if you use that particular lender--and you qualify financially--you may get very attractive financing. But always shop and compare.
Also, recognize that a lot of "extras" that builders sell (fireplace, finished basement, certain upgrades) cost the builder far less than he's charging you. So, sometimes, if a builder wants to move some houses, he can throw in those extras for nothing, or at a very reduced cost.
One other tip: Use a Realtor even when buying from a builder. It won't cost you any more, and the Realtor may be able to negotiate some things for you that you wouldn't be able to get on your own.
Another tip: Have a home inspection, even on a new home.
Hope that helps.