The following is an excerpt from page 16 of the Warhammer Annual 2002 release with an expanded explanation by Gav Thorpe regarding the how to handle pursuing/overrunning into enemies who have also charged.
It is possible that two units can end up in contact with each other and both count as charging. For example, two units may pursue into each other, or a pursuing unit might well run into the enemy and then get charged in the next turn. Normally a charging unit always strikes first, but in this situation what is the order of attacks? Well, after much umming and aahing, we've come up with the following solution, which is actually quite difficult to explain, but straightforward on the tabletop.
When a combat involves charging units from both sides, the chargers strike in the order in which they charged. However, models may not strike against an enemy that has charged them until that charging unit's attacks are resolved. All units striking first are allowed all the normal charge bonuses for lances, etc. A unit that has been charged and is not charging itself will always strike after all charging units - only the order of the chargers' attacks are relevant.
This sounds horribly complex but isn't really, and is most easily demonstrated by a nice example, so have a look at the diagram above. Note that Empire detachments have their own special rules so that when counter-charging they will always strike first. However, if not specifically counter-charging then the strike order below is used.
Order of Attacks
Unit b vs a will receive a charge bonus.
Unit c vs b will receive a charge bonus.
Unit b vs c does not receive a charge bonus.
Unit a vs b does not receive a charge bonus.