There are a few options, like anything if you want "the best price" you have to shop around. That said there are some options:
Go to the Disney web page, request the DVD and literature, that gets you on the mailing list and you occasionally get offers for special rates by mail that you may not get anywhere else.
Sign up on mousesavers.com for the free newsletter.
If you don't already have one apply for the Disney credit card, you will also get deals in the mail from them as well as the perks of extra Disney dollars and 0% financing on the trip.
If your a member of AAA drop by a travel center and checkout the deals regularly. AAA buys a lot of rooms in blocks and often has the best rates due to long standing agreements with Disney.
Contact a travel agent that specializes in Disney vacations. They have access to deals you may not have direct access to and sometimes can offer more on the side if they have a direct affiliation with WDW.
I never book directly on the Disney web site/Disney travel agency anymore, you can find much better deals elsewhere, but DO use it for trip planning.
I was very disapointed with the travel agency promoted by mousesavers, they basically told me to go to AAA they couldn't get me a deal when we wanted to go and if we couldn't find anything anywhere else call them back... this was after waiting over a week for a reply.... if I wanted to do it myself I would not be contacting a travel agent! grrr...
I have never booked with AAA since they seem to always be sold out of the times we want but the deals are reportedly the best IF you can get them before they are gone. If you can be flexible with the travel times (e.g. no kids or you can pull them out of school to get the best deal) this may be for you.
I have booked with Magical Travel (http://www.magicaltravel.com) a dedicated Disney Travel agency, they are not owned by Disney but are certified by them and have access to all the deals available from Disney and other travel agencies. For example they hooked us up with rooms at the Polynesian over thanksgiving week when AAA, expidia, Travelocity, and Disney told me there where no rooms available only a month before the trip. They also throw in Disney Dollars (I think it was $100 in FREE Disney dollars this trip) and autograph books for the kids, found us a great deal on an airline and arranged all the dining reservations etc for us. This will be the 5th trip using them and I strongly recommend them. They know disney and they know customer service and even if its the same price as the others you still get the free Disney cash and autograph book. The do all Disney parks and cruises and thats their whole focus, they won't try to sell you something you don't want.
AAA doesn't generally have the best prices, but if you have a AAA card, then that is a good place to start for room discounts if nothing else is out yet. AP rates, Florida Resident rates, those are usually the best - but more last-minute. Disney sometimes has room-only discounts, often has package discounts. Mousesavers really is a one-stop shop in pretty much everything. Disney Visa sometimes gives you a heads-up (a few extra days) to book, but not much else anymore.