Really, this is the hidden price of being evil, or being perceived to be evil, but nice rhymed so I went with that instead. I was discussing party reputation with Keir's player the other day, and I commented that evil parties tend to accumulate a LOT more gold than their good counterparts. This is simply a matter of essential nature; many evil characters won't work unless they feel they're getting something in return—or a lot in return, such as treasure.
Good parties tend to do things for much less money. They generally feel bad taking from people when the cause is right—or at least, they'd rather not bankrupt them or push their luck. Good adventurers do things to make the world a better place (usually) and that means they're often satisfied with much smaller stipends. Sometimes they do work for free, or for non-gold rewards (potions, spells, etc.) which evil parties are, for some reason, far less inclined to do.
It would seem, at surface glance, that evil parties therefore have a major benefit right out of the gate. After all, having an additional 10-50% in your coffers can make for a massive differential in power. However, this is only an apparent advantage. Good parties generate reputation very well for the most part, and people are generally willing to help them out out of a sense of duty, friendship, or kindness. Evil parties generate much less good will by that same nature. Evil NPCs are generally untrusting, requiring large fees to get into motion.
Now, that's not to say that good characters will never fleece each other, or that they can't be recalcitrant or grumpy. However, more people will be inclined to be nicer to a party with a good reputation (or a reputation for kind acts &etc).
This brought us to the following decision: there is an unseen differential that acts as a sort of hidden exchange rate during all transactions. This is the party reputation. While good parties may be shorter on gold, their reputation usually allows that gold to go farther. Thus, reputation can act as a modifier on the purchasing power of the coffers themselves.
Thus, let us say that The Silencers (an evil party) have 100,000gp in their party banks. They earned this through stealth, thievery, bribery, and outright murder. They are feared and hated, and some folks will refuse to even serve them (if they aren't so afraid of them that they do). We'll list their reputation as -50. The Hounds, however, have been extremely altruistic. They have managed to make 30,000gp but they are well-loved. We'll say their reputation is 50.
A sample transaction: The Silencers want to buy the services of a local wizard. The spell going rate is 10,000gp. When their reputation is applied, however, we must multiply the cost. -50 implies a 50% raise in price, leaving them with a 15,000gp spell. The same works in reverse for the Hounds; the spell costs them 5,000gp. This leaves a gap of 10,000gp between them, fully the entire original price of the spell. Thus, the Hounds have an adjusted bank of 60,000gp in this case, and can likely get other services completely for free.
Of course, this is a gross oversimplification. Positive relationships with one group imply negative relationships with another, as politics is almost always zero-sum. Evil groups will get in close with evil people, which will mitigate this effect. Yet, even so, evil NPCs are less likely to give away anything for free while the reverse is not true of good NPCs.
Thus, I would say that the two reach an unsteady balance—in theory. In practice, of course, the morass of variables means that every party interacts with the world in a completely unique way.