Any basically, usually prefer both of them beign from same faction. Also as the exception, the noob combo ( plasma pistol and magnum). Also in some cases (depending on level or if its in multiplayer) other thats good against shields and other against unshielded or precision weapon.
Depends on the situation and its about the user. Also not so good weapon is better than empty one. Unless melee is most effective strategy at the time and weapon has more useful/powerful melee like Halo 2 brute shot as one.