This is a good topic, but somewhat challenging. For search the reviews here, and you'll see thumbs both up and down on just about every restaurant, so as others have pointed out, defining "under rated" isn't as easy as it seems. Given all that, here's my short list (which probably is just as much a list of the best "overlooked" dining spots):
Park: I agree with Mike n Kathy, the Tangerine Cafe in Morocco In Epcot. Some of the most creative (and tasty) fast food in all of WDW. I've hardly ever seen this place mentioned in trip/dining reports, but when it is, it often gets a thumb down (from meat and potaoes types not familiar with/frightened by "foreign" food).
Hotel: the Concourse Steakhouse in the Contemporary. While offering some of the best beef on property, this restaurant is continually underrated due to its location (right below the monorail; kids enjoy that, but some feel it's an inappropriate spot for "fine dining.")
Downtown Disney: Portobello Yacht Club. Menu goes in the direction of Spoodles at the BW, but is better prepared and delivered (great service). Like the Tangerine Cafe, the Portobello hardly ever gets mentioned on the DIS (perhaps suffering from its location next to continually delcining PI); the few reviews I've seen primarily whine about long waits for walk in seating (earth to the whiners...learn the meaning of AR.....)
Outside WDW (but still a Disney restaurant): Shutters at the Disney Vero Beach Resort. The Continental style menu at this cute little bistro is suprisingly broad and of much higher quality than one would expect at such a laid back resort. And hardly anyone on DIS ever mentions the place....