Don't listen to the haters, people. Jacksonville is a great town -- just don't expect it to be New York or New Orleans or whatever when it comes to good eats.
And if you're staying downtown, be prepared to drive a ways to get to most decent restaurants -- it's a pretty far-flung town, and the city center's not much to speak of.
Jerseygirl's recommendation of the Outback Crab Shack is spot-on -- it's on County Road 13 in St. Augustine, which is a decent drive, but won't kill you. It's entirely worth it.
The Chart House on the river, once J-ville's signature quality restaurant, has fallen on hard times after an ownership switch, and isn't as good as it once was. But it still beats Chili's, or whatever other chain you were thinking about visiting. There's also a decent little microbrewery restaurant on the south side of the river whose name escapes me -- quite good, right by the I-95/I-10 interchange.
Rumor has it that Gordo's, a tasty Cuban place downtown that was only open for lunch, has now closed. The world is a sadder place.
At the beach, Mezzaluna on 3rd street in Atlantic Beach is pretty solid Northern Italian fare -- again, keeping in mind that you're not in New York, much less Rome. Tra Vini in Ponte Vedra, just a little ways down A1A, is also good.
If you're staying in the Southside/Baymeadows/Mandarin area, there's a big new development on Southside Boulevard south of Atlantic Blvd. If you're looking for chain-type restaurants, that's the place to go -- decent Japanese steakhouse-y place, a couple of good seafood restaurants, and some burger/sandwich joints. Another good place to get similar fare is around the Avenues mall, near the I-95/I-295 interchange -- there's an Applebees, an Olive Garden, etc.
Oh, and for those of you working for generous companies with enormous expense accounts -- not that such a thing exists -- I should point out that Jacksonville has two Ruth's Chris steakhouses (the one in Ponte Vedra's better than the one downtown) and a Morton's downtown.
Enjoy the Super Bowl, and try not to hate overmuch on the town.