It's really hit-and-miss when it comes to what is available. In MK, Casey's does have kraut and free cheese sauce. At Cosmic Ray's, they have a full topping bar and have brought back the free cheese sauce as well. (For about a year it wasn't on the topping bar, you had to ask for it for a fee.) Cosmic Ray's has the most items I think followed by Peco's Bills which is almost as complete. Pinocchio's has just condiments since they got rid of their burger offerings a few years ago. The Harbor House offers condiments - including honey mustard - but no "toppings."
Over in Epcot, however, things have gone crappy. Electric Umbrella took away their topping bar when they brought in the do-it-yourself drinks. The up is that you get free refills. The down is that the burgers come loaded and if you don't want that, you have to ask. If you want anything different or special, you're out of luck. The Liberty Inn still has a "topping bar" but it's useless as it has only condiments and lettuce and tomato. You can't even get honey mustard there any more. (You have to get it from the counter.) Which is silly since they sell chicken nuggets there now and a lot of people want honey mustard with them. And if you get a CM who doesn't know better, they'll tell you it's not available at all even though we've gotten it from the counter.
I don't eat quick service at the Studios since it sucks so I can't tell you what they offer recently. (I do know a few years back I asked about cheese sauce and said, "MK offers it" and the CM said very grumpily, "we're not magic kingdom." Oookay. You couldn't even buy it at the time. Don't know if that's changed or not.)
And I'm rarely in AK for meals but off the top of my head, I can't think of any topping bars. I might be wrong though.
Best bet would be Cosmic Ray's or Peco's Bills in MK. They offer the most items and biggest selection.