After sifting through all manner of old rules books, I've seen nothing written about firing missile over or through friendly characters. I find this quite odd, as it's a scenario I see all the time, particularly in dungeons. As an example, a party is walking down a typical 10 ' wide hallway. The front rank is composed of fighters, probably with shields. The second rank may be composed with others with long spears or pole arms. Rules for attacking with these sorts of weapons are fairly clearly explained in most rules. However, what if the second rank is composed of archers, or PCs wishing to throw oil or javelins? Here the rules are unclear. In 3.5, there is a -4 penalty if you draw line of sight through an ally, but that seems quite excessive when the characters are in set ranks.
How are other DMs handling this situation? Currently I'm not placing any penalties on characters firing from the second rank as long as their targets are not in melee. But I have been thinking of placing a -1 or -2 penalty if the front rank is involved in melee, or if the front rank consists of characters that are taller than the second.