You probably have noticed that the 3E core books don't say anything about recharging staves and wands. The idea came up during the development of 3E (after all, it was present in some form or another in 1E and 2E), but the core designers eventually discarded it. Noticing this, I asked Monte "Why can't a spellcaster recharge a staff or wand under the new rules? It would be cool if he could do that." He replied, "Because it's already cool that he can make the staff or wand in the first place."
While that may seem an odd answer, there is a game rule reason for this decision: if characters can already makes staves and wands for cheap (per charge, spell trigger items are about half the cost of a scroll and about 1/3 the cost of a potion) and you allow them to recharge those items (presumably at a discount because "some of the work in creating the item is already done"), it makes those items even better, and they're already some of the best magic items in the game in terms of value for your money.
Allowing a discount for recharging also makes it really hard to determine the market price of the item, as you have to add up the value of the originally-crafted charges remaining and the value of the recharged-charges, which forces the user to keep track of whether a charge is original or recharged (despite them having the identical effect).
However, it doesn't seem logical in-game that a powerful wizard would create a staff of power, use all of its charges, then throw it away like an ordinary stick. It makes more sense that he'd pour more power into that staff and carry it around for most of his adventuring career. Fortunately, the 3E rules already handle adding additional magic abilities to an existing magic item, and we can use those rules to let the wizard recharge his favorite staff: just determine the difference between the current item's value and its value with the new abilities (i.e., its value with the added charges), and spend time, XP, and gp based on that difference. Example: A full-charged staff of power has 50 charges and a market price of 211,000gp (according to the 3.5 DMG), or 4,220gp per charge. If the staff currently has 10 charges (market price 42,200gp) and its owner wants to add two charges to it, that's a difference of 8,440gp. Recharging these two charges takes him 9 days and costs 4,220 gp and 337 XP.
(Given, the staff of power is an imperfect example because it has properties other than its charge-based stuff, like its enhancement bonus, and thus the value of its charges shouldn't have a linear dependency on the item's total price, but for simplicity's sake I'm going to ignore that.)
There's still a small problem with using the standard item-improvement rules, though, and it has to do with how cheap the per-charge cost is: it's so cheap to add charges that it makes using Brew Potion and Scribe Scroll obsolete. It's more cost effective to add a single charge to a wand or staff than it is to craft a potion or scroll with the same effect.
Example: A wand of fear has a DMG price of 21,000gp, which works out to 420gp per charge (market price). A potion of fear* has a market price of 1,400gp. A scroll of fear is 700gp. Either way, the wizard is smarter to recharge the wand rather than crafting a new potion or scroll. Heck, the wizard could add two charges to the wand in the same amount of time (1 day mininum to create an item, 420gp per charge x 2 charges = 840gp, which is under the 1,000gp cap for one day's work) it takes to make the potion or scroll, so he's way ahead if he chooses to recharge. Any time the owner has a day of downtime, he's likely to drop a little money and add a couple of charges to the wand, which trivializes the importance of the magic item.
* Ignoring that you can't make a 4th-level potion and you normally wouldn't want a potion of fear (as under some interpretations of the rules the potion would target you)....
How to avoid this almost-loophole without hosing the wand- and staff-makers? Require a minimum number of charges, which increases the minimum investment of time and money into the item. While this limitation doesn't have an effect on the weakest spell-trigger items, it does keep the spellcasters from using their "spare change" to charge up their strong wands and staves (for example, it costs 4,200gp to add 10 charges to a wand of fear).
So here's the variant rule:
Variant: Recharging Spell-Trigger Items|
A character may recharge an existing staff or wand by using the craft item rules to increase the number of charges in the item. Divide the item's market price by 50 to determine the price per charge. Multiple the price per charge by the number of charges the character is adding to determine the total cost of improvements for the item; determine time, gp, and XP expenditure normally based on the improvements cost.
The character must add at least 10 charges to the item with each recharging.
The character does not receive a discount for recharging the item (the cost per charge for recharging is exactly the same as if she were creating a new charged item of similar type).
This makes staves and wands a little more useful (not that they need it) and should silence most complaints about not being able to recharge these items. You don't get a discount, but it's still cheaper than making a brand new item.