Are there any rules for using a Longbow in parabolic flight, e.g. when you don't have Line of Sight or the target is a very long way a way?
There is an argument to be made that longbows' range already assumes parabolic flight when possible. If you buy that idea, there is a built-in rule for handling the difficulty of attacking targets that are out of sight: Concealment. See the Player's Handbook v3.5, p. 152, or total concealment in the d20 SRD.
Because you have to target a square where you think the enemy is, you're not going to hit if you guess wrong. That naturally encourages massed fire, with as many archers as possible targeting many squares near the assumed position of the enemy.
Heroes of Battle, pages 68 and 69 talk about volley fire and indirect fire.
While researching longbows recently (for the sniper article) I found an excellent quote from wikipeida:
The longbow had a long range and high accuracy, but not both at the same time. Most of the longer range shooting mentioned in stories was not marksmanship, but rather thousands of archers launching volleys of arrows at an entire army. Longbowmen armies would aim at an area and shoot a rain of arrows hitting indiscriminately at anyone in the area, a decidedly un-chivalrous but highly effective means of combat. An archer could hit a person at 165 m (180 yards) "part of the time" and could always hit an army.
From this the HoB rules should be very sufficient for your needs, as players would find it incredibly difficult to perform extremely long range or indirect fire precision archery without some kind of seeking arrow.
If they do want to mimic artillery, there is no better PrC than arcane archer (except for arcane archer ported to the psionic rules). Imbuing an arrow with fireball then lofting it in an indirect arc with help from a spotter is an excellent way to simulate a howitzer.
Most wargames and a few RPG games use a scatter diagram and relative degree of success to represent indirect fire.
Basically you are at a minus (sometimes considerable) when you roll you are seeing if you hit a designated area. If you miss you still hit an area but at some distance from the target. For d20 based systems I recommend assigning an addition -3 modifier in addition to range. For every one you miss by you shift one hex or square. You are shooting to hit Armor Class 10.
If you are using hexes roll a d6 to see which hex face you shift.
If you are using squares then roll a d8 to see which direction you shift.
If there is a target in the square Then make another to hit roll. No modifier you are looking to beat the person's AC or roll a nat 20 (if it is higher than 20). This represents the chance whether the arrow penetrates the armor and is basically pure blind chance. If the arrow magical then apply that bonus to this roll.
Again the first roll is to see whether you hit the target area. The second whether the arrow penetrates the armor.