We keep copies of the characters sheets, so that if someone is missing the other players just play them as an NPC. If several players missing I usually come up with an excuse to temporarily split the party up into two groups, and just focus on the ones that are there.
We once had a player who was away at college, and could only make the occassional game. His character liked to drink, and soon acquired himself a Pooka, which worked as a great plot device to remove and then reinsert the character.