It's been a while since I've run a game (or played in one, actually), but it's something I've worried about from time to time. I've got a few contingency plans just in case - since most munchkins seem to favor combat prowress, players should expect more adventures to pop up where diplomacy and/or espionage are the key to success. Then again, in the game I ran that my players seemed to enjoy the most, the campaign was custom-built around the characters they created. Although I did have an overriding story, there were often instances where NPCs, events and settings were shaped directly by the players' actions - often in ways they weren't expecting and sometimes regretted afterward.
Thinking about my own characters I've played, I've made an amusing observation. It seems like I tend to lean towards being an "anti-munchkin," in the sense that I'll often try to deliberately hamstring or limit my character. (Such as, in the 3.5 D&D rules, making a half-orc bard - yes, the player race with the penalty to Charisma and one of the classes that needs it the most). Why? To make the character more interesting!
Fathom123 summed it up quite well. Story before stats.