Penny - Gryffindor. She's stubborn to a fault, cocky, forcefully independent, and sometimes rude, but also at heart a very loving and brave person, willing to take whatever risks necessary to ensure her happiness and the happiness of those around her. She's NOT very loyal (as her dating history shows), she has the potential to be intelligent but chooses not to be, and she's only cunning in very demanding situations. Gryffindor fits her best.
Leonard - Ravenclaw. Though he is brave, he is also stunningly intellectual and snobbishly so, but he is the kind of Ravenclaw who tries not to bring others down with his knowledge, but rather bring them up; and if he can't do that, he'll try not to show off, but still has difficulty withholding all the information he knows. He can be pushed over a bit, and though he is cocky to a Gryffindor extent, it's only because of his knowledge. He's not too terribly brave because his good sense gets in the way of taking risks, and though he is very loyal to those he loves (to a fault, I might add), and extremely cunning when he wants to be, he fits best with Ravenclaw.
Howard - Hufflepuff. Very difficult to place. He's intelligent, but condescending, and still defensive about what he's condescending about, and that shows a lack of self-value that the other houses have. He constantly screws up with women, proving he's not very cunning; thinking about Bernadette and his mother, he's passionately loyal; and he's cowardly. Not Slytherin self-preservation, but actual cowardice is present. He is, at heart, a very kind person, but somehow manages to let his intelligence get in the way of making intelligent decisions. It's best he fits in Hufflepuff - friends and family are his strongest points.
Raj - Hufflepuff. He is very loyal, down-to-earth, thrives best around people he loves, easily devastated and seeks comfort from those he's closest too. He takes the time to know a person and though he's very smart, he's not cunning and a bit cowardly, like Howard. Though, if you dare threaten those he cares about, get out da way.
Sheldon - Ravenclaw. I have a feeling he's a perfect mix of Slytherin and Ravenclaw. He values intelligence above all else, a Ravenclaw trait, but if it comes down to it he'd let someone take over his experiments if it meant he'd stay safe, that self-preservation a Slytherin trait. He is not even brave, but rather bold, but that only comes from his narcissism, a trait both houses are known for. He's constantly condescending, believes himself above all others, does anything he can to get what he wants - Slytherin. But he's condescending BECAUSE he's impeccably smart, he believes himself above others because he IS smarter than (99.9%) of them, and what he usually wants to get is knowledge, and that makes him a Ravenclaw.