Best run would be a toss up between a few companies for me.
GE has been a rock since Welch came on board- fiercely competetive, shrewd, and picks its battles to win. It's so widely diversified and large yet amazingly has relatively little beaurocracy because of the way it is structured.
Dell has been a model business success story in sheerly outplaying its competition. It's smarter, stronger, and quicker than its competition. Which is amazing considering the cutthroat nature of its industry and the fact that it was an unknown name to most people 10 years ago.
SW Air manages to pay its employess the WORST salaries in the airline business and yet has the HAPPIEST employees in the airline business. You just have to respect a company that can do that. Not even to mention the fact that it has been a financial model airline and epitomizes efficiency.
Companies like MS and Cisco wouldn't qualify as the best run for me because they won their success based on being the first ot market with a killer product. As a result they were able to all but monopolize them and derive enormous margins. A company like MS can run itself like crap and still bring in billions because of the strangehold it has on PCs.