We honeymooned at Disney World, and it was amazing!
We paid to upgrade to the deluxe dining plan so that we could also eat at some of the really nice restaurants that cost two meal credits. If doing that is in the budget, the California Grill is AMAZING, and so is Narcoosee’s.
If you’re sticking with the regular plan, my favorites for a Honeymoon are…
Magic Kingdom – Be Our Guest is a new restaurant themed around Beauty and the Beast, it’s supposed to be really cool! Eating in castle is cool too, but more for the environment than the food.
Epcot – Le Cellier is a must! It’s the steakhouse in Canada – I’d go for lunch, dinner takes two meal credits and you can get the same food at lunchtime. Although really just about anywhere in the World Showcase is cool, maybe pull up the menus online (you can see them at http://www.wdwinfo.com/wdwinfo/dining/disneydining.cfm) and see what sounds good. Other than Le Cellier, I’ve heard the best things about Chefs de France (French food, obviously), Restaurant Marrakesh (Moroccan), Teppan Edo (Japanese, you’ll sit with other families/couples, one of those cool setups where they cook the food on the grill right in front of you), and Via Napoli (Italian). For seafood, the Coral Reef is great and you’re surrounded by an aquarium.
Hollywood Studios – I’m going to have to disagree with the Sci-Fi recommendation, the environment is cool but the food is pretty awful. 50s Prime Time is funny and cool as long as you have a sense of humor about the waiter/waitress picking on you, haha.
Animal Kingdom – Flame Tree Barbecue, Yak and Yeti, and Tusker House are all great!
Hotels – I agree that Boma is great and really unique! Citricos in the Grand Floridian is very nice if you can’t spring for Narcoosee’s. The Kona Cafe at the Polynesian has a super popular breakfast food called Tonga Toast that tons of people, including my DH, love. Also at the Polynesian, the Spirit of Aloha Dinner Show is really cool!
Downtown Disney – Raglan Road has great Irish food, step dancing, etc.