First open the Freelancer Directory. Then open C:\...\DATA\EQUIPMENT\goods.ini
Find a ship you would like to change the price. Use the Freelancer Database to find your ship nickname. To find the ship nickname press CTRL+F in the goods.ini file and enter the ship nickname. It will come up at the location of the entry.

You will see something like this (I'm using the Anubis in this tutorial) :
[Good
nickname = oe_hull
category = shiphull
ship = or_elite
price = 1200 <----------------Change this to whatever you want the ships price to be
ids_name = 12019
item_icon = Equipment\models\commodities\nn_icons\or_fighter.3db

You will change the price for that ship at every base it sells at.

That will only work to a certain degree, if you want accurate prices over 10 million, it's better to edit the exe file to display prices correctly, which is explained elsewhere

Well there is a way to make a ship cost more than 10 millions. You hav to make the cost 9.999.999 and then add make the reactor or the engine cost a lot and voila, you have a ship that costs (more) than 10 millions