You can charge as many times as you want, provided you're in the right conditions (enough distance, no obstacles in your path) and you have enough time to do the action (with a Belt of Battle or on a high-level factotum you could do it even twice in a round).
The Dire Charge epic feat, the Catfolk Pounce feat from Races of the Wild and the Pounce special attack from some 3.0 monsters can only be used during the first round of combat. Maybe your "source" is based on one of these.
There aren't any.
(At least not in the core Players Handbook or Dungeon Masters' Guide)
You will have to work with your GM (or players) to figure out how to adjudicate nonmagical flaming arrows.
There are, however, rules for using other sorts of fire as a weapon.
- A full pint of oil is an improvised thrown weapon with a 50% chance to behave as alchemist's fire does, and a 50% chance to do nothing.
- A torch is an improvised weapon and deals only 1 point of fire damage beyond the bludgeoning damage of being hit with a torch.
- Blunt Arrows (Races of the Wild) have a 30' range increment.
(Note: Improvised weapons suffer a -4 penalty to hit)
We can also consider the historical use of actual flaming arrows.
There is a well researched and easy to digest wikipedia article on the subject.
When flaming arrows were used, they were created by soaking a cloth in some kind of flammable material, and wrapping it around the head (like a torch). The result is not only heavier than an arrow, and blunted, but also padded, and utterly ineffective against things that don't burn well, like people. Fire weaponry was primarily used to destroy crop-fields, tents, thatch-roofed buildings, and other flammable material possessions. They were a strategic weapon, not a combat one.
Taken together, I would adjudicate flaming arrows as being equivalent to ranged torches.
And add specific rules for setting objects on fire, since that's what I expect them to be used for.
A flaming arrow suffers a -4 penalty to hit, has a 30' range increment, and deals damage equal to a gauntlet of its size category, plus a single point of fire damage. It also can ignite flammable objects where it lands, if not removed or extinguished. Oil and similar substances ignite instantly, dry grass, thatch, or cloth ignites after one round, and wood ignites after 1d4 rounds. Removing or extinguishing a flaming arrow before it ignites its target is a move action ("pick up an item") which provokes an attack of opportunity.
This is, however, homebrew, and not RAW.
Best Answer
You unwittingly have two different questions without realizing it.
Question 1: How do I avoid injuring my allies with the Prismatic Burst on my melee weapon?
Answer 1: Easily. The Prismatic Burst weapon enhancement only affects the target of your confirmed critical hit. "Whenever you score a successful critical hit with this weapon, . . . , subjecting the target to a prismatic spray effect." You do not get a free casting of the spell on an area, but just an effect on a single target.
Question 2: How do I avoid injuring my allies with area-effect spells?
Answer 2: By spell selection and tactics. This can be a big and dramatic part of D&D 3.5 tactical combat. One climactic moment in a game I played involved me defeating our opponent with a fireball that killed one of the party, but saved the rest of us from almost certain doom. Those using area effect spells also generally choose their zones very carefully to maximize damage to the enemy and to avoid injuring allies. While the tactics are not historical in any way, this does lead to in-game tactics of spreading apart and using cover. Regardless, you generally cannot fireball into a melee without endangering your allies: it's one of the trade-offs.