I may have taken the extreme position here: I've lowered the cost of scribing to spell 1 gp per spell level.
I can only see a couple of reasons for the "by-the-book" costs:
1. To constrain the wizard's spell selection. He might have a large pool of spells from which to choose, but has to choose carefully, since he can't afford them all.
2. To reduce a wizard's money, treating spellbooks as an item just like a fighter's sword.
Here's my approach to each of these:
1. As DM, _I_ constrain my campaign's spell availability. In our campaign, magic as a "rare and wondrous thing". There are few stores that sell magical items, and they typically don't have more than a few outrageously overpriced low level scrolls. PC wizards treasure spells because they're hard to find, not because they're expensive. Even if a wizard does find stacks of scrolls, he still needs to find time to scribe them, and needs to be in a large enough city to buy the special inks and materials.
2. Personally, I don't find that "forcing" a wizard to spend most of his wealth to cast spells to be equitible. Yes, fighters need equipment, but there's a huge difference of degree here. A fighter can buy off-the-shelf armor and weapons, and still contribute significantly. A wizard without a spellbook is basically crippled. Does this increase the power of a wizard over a sorcerer? Maybe: it results in more equal wealth across classes to spend on other items, potions for the party and so on. In our campaign, the end result has been the wizard taking item creation feats and crafting weapons for the rest of the group.
In a nutshell, I think there are many, many other ways to control player wealth, and limit a wizard's known spells. Over-inflating the cost of his most basic tools seems, well, silly. A spellbook should be valuable for the knowledge it contains, not the cost of the ink.
Of course, as others have eloquently stated, this decision depends heavily on your campaign, levels of wealth, spell availablilty and so on. It's worked well for us though.
--shaele