It's hard for any of us to really tell you where you should go since they all have their ups and downs...
We have eaten at 50's Primetime Cafe, Mama Melroses and Sci-Fi Drive In. Out of those, I would only go back to the 50's because the Sci-Fi food wasn't that good (in our opinion) and Mama Melrose's service was lack luster (and I got sick).
Hollywood Brown Derby is supposed to be incredible, but very $$$.
I would take advantage of the links that were provided already, check out their menu's and see what food appeals to you the most... If you are having a hard time deciding between 2, do lunch at one and dinner at the other...
Don't forget that some of these restaurants also give you a priority seating option for Fantasmic, which means you don't have to get to Fantasmic hours before it starts just to get a good seat.. You pay 1 flat rate and get 1 PS for both dinner and the show.. We did it last year and had pretty good seats, but it wasn't overly crowded when we were there and probably could have just taken our chances with the normal seating section..
I'm sure you'll be happy with whatever decision you make. Have fun!!!