Congrats on your honeymoon!
Are you looking more for romantic or fun? In additon to the ones listed....
Romantic: California Grill, Narcooses or Ctricos, Victoria & ALberts ($$$, I've not dined there but it pretty consistently gets great reviews), Chefs de France or Bistro de Paris, San Angel Inn
Fun: Beaches & Cream for dessert (we walk over after Epcot closes), Sci-Fi, 50's Prime Time
Misc: Kona Cafe (dessert is great as are all the meals), Teppenyaki, Tony's Town Square
My husband and I honeymooned in January 2000. One thing we did was make our PS for the last seating each evening. We did that because the park hours were short and we wanted to not have to stop during the precious hours. As it turns out, that was one of the best things we did. Several of them turned out that we finished after the park hours, so we'd come out to a mostly-empty park. It was great to come out and feel like we had the park to ourselves as we wandered out.
A couple nights we went to the Kona Cafe and got dessert to go (we've also gotten dessert from the snack-bar place in the Poly). We took it down to the beach and watched the Electrial Water Pageant parade from there. Very nice.

We've done the same at GF but with ice cream from their snack-bar.