I have stayed at the Courtyard, the Wyndham, and the Hilton. My overall recommendation would probably be the Hilton, unless you were definitely wanting spa services, such as facial and body wraps, etc., which only the Wyndham has. Here's my views of them all:
The Courtyard definitely has almost a motel feeling to it, even with interior corridors LOL. The services are very limited there, the rooms are very generic, fitness center is not really usable for a serious workout, the pool doesn't seem to be heated- but, you can often get this resort for around 30 bucks if budget is your first concern- probably the least expensive hotel on Disney property. Nothing really wrong with it, but just not as many services and not as fancy as the others (no bell services, no valet, no 24-hour deli, etc etc). Also a little bit of a hike to walk to downtown disney.
The Wyndham bills itself as the fanciest of the downtown disney resorts, and does have a rather upscale spa and fitness center based on a very exclusive spa out in California. The lobby is very old-money, with tapestries and grand piano, and grand-looking bar and library. This hotel is the tallest, at 26 stories (? correct me if wrong on the number of stories, but that's close), and has an exclusive eatery on the top floor. On the down side, looking around this resort, it really does need some refurbishment--a lot of the real wood doors have large and noticeable scratches, the carpet looks old, the furniture and bedspreads seemed a little over-the-hill, etc. If they would even put a reasonable amount of money into redoing this resort, it could rival the Disney deluxes in luxury, but right now it's a little tired. It is right across the street from downtown disney (although not quite as close as the Hilton), and has everything you would expect from a deluxe, swimming pool with waterfall, tennis courts, fitness center, 24 hour room service and deli, and holds the nice distinction of being the first stop on the downtown disney bus system to the parks.
The Hilton building looks kind of garish and a little tired on the outside, but once you walk in you're pleasantly surprised. Everything here has, or at least looks to be, recently renovated and spotless. It has most of the amenities of the Wyndham, including a nice pool that's actually deep enough to dive in, 24 hour room service and deli, a nice usable fitness center, second on the bus line, and absolutely spotless rooms. I've stayed there more than once, and the rooms were always about the cleanest hotel rooms I've ever been in, almost as though I were the first person to stay there after the renovation. The rooms have two vanity areas, one inside the bathroom and one outside, each with it's own sink. The Hilton also has the nicest Disney gift shop that I've seen for any of the downtown disney hotels, although you don't need it, since there is a walkway right behind the pool that takes you maybe 100 yards to Downtown Disney (very short walk- you walk around the trees in back of the pool, and whoa! There's the shops right across the street! You don't realize how close that pool is to the road LOL). So even though the Wyndham is more of a spread out resort with a few more of the upscale-type amenities, I would still recommend the Hilton, because of the condition of the rooms (almost disney-like decor), the overall condition of the resort, and the even closer walk to downtown disney. I guess it really depends on whether you would like the fancy spa services of the Wyndham, or also if you would like a balcony (almost all rooms at the Hilton do not have a balcony, while most rooms at the Wyndham do, although that's no guarantee you'll like what's out there LOL) Anyway, this should give you an idea of what the resorts are like, and you can pick the sort of one you're most comfortable with.