As others have mentioned, Joe's (for the pulled pork, which isn't really what most people consider normal KC-style BBQ, but it's what they're known for--also, the Z-Man sandwich is great) and LC's for the burnt ends (very much a KC thing). I prefer the ribs at Jack Stack (and I'm not much of a rib person, so they have to be really good for me to like and bother with them) and don't recall being all that impressed with Arthur Bryant's, though it's been years since I've been there.

Pecan Lodge is Central Texas-style (though they do pull some outside influences in). In Texas, they believe that real barbecue (which, to them, is mostly beef) does not need sauce. If the meat is done right, the flavors imparted by the smoking process are good enough to eat alone, and sauce would just cover the masterpiece up. Thus, it's very different from NC-style BBQ (both eastern and western), since one of the big hallmarks of NC-style BBQ (and differentiation between eastern and western) is the base of the sauce, and in Texas barbecue, sauce is an afterthought at best. (Also, NC seems to be all about the pork.)

The brisket at Pecan Lodge was the second-best I've had ever, after Franklin. But--they also did an excellent job on the burnt ends, the pulled pork, the pork ribs, and the sausage--all things that aren't wholly native to Central Texas-style BBQ. (In fact, if you're going by overall quality, I might actually say that I prefer Pecan Lodge to Franklin, since while Franklin has truly brought brisket to an art form, the rest of his meats are inconsistent, in my experience.)

Having traveled fairly extensively around Texas, Missouri, and the South, I've had the chance to sample a lot of barbecue (and a lot of well-known, nationally-famous 'cue), and very few instances stand out in my memory like Pecan Lodge does.