Right from the beginning I get this feeling that Sheldon actually secretly respects Howard most of all. If you notice, in most of the cases, Howard is the one who stands up to Sheldon and can confidently oppose his ideas, while Raj and Leonard most of the time just take it for granted that Sheldon's smarter than them. Being an engineer, Howard has something none of the others do: practical skills and Sheldon's very well aware of this. He knows Howard is brilliant in a field which requires an entirely different set of skills and something he can never be. He probably doesn't respect engineering but he does respect Howard. Also, most of the stuff that they make and do is dependent completely on Howard, like that "killer" robot.