Well, there's shield, of course, as well as the brooch of shielding. Lesser globe of invulnerability works (as does similar spells), as does an antimagic field, the spell Nightshield (Spell Conpendium 3.5), Spell turning is an option 2 I think .
You can counterspell it with magic missile or dispel magic. A ring of counterspells can be used by non-casters.
You can boost your spell resistance to negate the spell.
Mirror image or any other spell/effect that makes you seem to be in one place rather than where you are can be useful as well. However, blink, et. al., do not work as force effects extend into the ethereal plane.